Starting phenix.real_space_refine on Wed Aug 27 01:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssl_40751/08_2025/8ssl_40751.map" } resolution = 4.6 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= 0.260 sd= 0.795 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24405 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 15357 2.51 5 N 4454 2.21 5 O 4743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24672 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8193 Classifications: {'peptide': 1072} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1035} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8197 Classifications: {'peptide': 1072} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1035} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8197 Classifications: {'peptide': 1072} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1035} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.25 Number of scatterers: 24672 At special positions: 0 Unit cell: (127.984, 134.383, 206.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 6 15.00 Mg 1 11.99 O 4743 8.00 N 4454 7.00 C 15357 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: 2.13 Conformation dependent library (CDL) restraints added in 882.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 57.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.779A pdb=" N TYR A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.097A pdb=" N ILE A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.589A pdb=" N ALA A 165 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.612A pdb=" N ALA A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 238 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.581A pdb=" N ALA A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 345 removed outlier: 3.790A pdb=" N ILE A 345 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 4.194A pdb=" N PHE A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 448 through 485 removed outlier: 3.613A pdb=" N GLU A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.507A pdb=" N TYR A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.645A pdb=" N ILE A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.853A pdb=" N TYR A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 708 removed outlier: 4.285A pdb=" N GLN A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing helix chain 'A' and resid 734 through 742 removed outlier: 4.505A pdb=" N GLU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 787 through 808 Processing helix chain 'A' and resid 812 through 820 removed outlier: 3.731A pdb=" N ASP A 815 " --> pdb=" O HIS A 812 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA A 817 " --> pdb=" O ASP A 814 " (cutoff:3.500A) Proline residue: A 818 - end of helix Processing helix chain 'A' and resid 831 through 850 removed outlier: 4.426A pdb=" N GLY A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 846 " --> pdb=" O ILE A 842 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 876 through 893 removed outlier: 3.858A pdb=" N ASP A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 884 " --> pdb=" O ASP A 880 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 928 removed outlier: 4.155A pdb=" N ARG A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 941 through 965 removed outlier: 4.304A pdb=" N GLU A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 removed outlier: 3.591A pdb=" N GLY A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 995 Processing helix chain 'A' and resid 1023 through 1041 removed outlier: 3.868A pdb=" N HIS A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1058 Processing helix chain 'A' and resid 1061 through 1070 removed outlier: 3.758A pdb=" N ASP A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1086 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.593A pdb=" N HIS B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 removed outlier: 4.349A pdb=" N ILE B 119 " --> pdb=" O GLY B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.620A pdb=" N VAL B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 238 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.020A pdb=" N GLU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 6.053A pdb=" N MET B 347 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 380 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.767A pdb=" N ASP B 388 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 418 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 448 through 488 removed outlier: 3.557A pdb=" N GLU B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 505 removed outlier: 4.454A pdb=" N GLU B 495 " --> pdb=" O SER B 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 505 " --> pdb=" O ARG B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.558A pdb=" N TYR B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 525 " --> pdb=" O GLN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 603 through 615 Processing helix chain 'B' and resid 628 through 633 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 656 through 664 removed outlier: 3.947A pdb=" N MET B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 664 " --> pdb=" O MET B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 708 removed outlier: 3.744A pdb=" N GLN B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 Processing helix chain 'B' and resid 734 through 742 removed outlier: 4.456A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 739 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 766 Processing helix chain 'B' and resid 778 through 785 removed outlier: 3.631A pdb=" N GLY B 785 " --> pdb=" O ILE B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 808 Processing helix chain 'B' and resid 812 through 816 removed outlier: 3.938A pdb=" N ASP B 815 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 816 " --> pdb=" O ILE B 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 816' Processing helix chain 'B' and resid 831 through 849 removed outlier: 4.068A pdb=" N GLY B 836 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 843 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 846 " --> pdb=" O ILE B 842 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 849 " --> pdb=" O VAL B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.786A pdb=" N LYS B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 893 removed outlier: 3.985A pdb=" N ASN B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 885 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 886 " --> pdb=" O ARG B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 927 removed outlier: 3.669A pdb=" N ARG B 917 " --> pdb=" O GLU B 913 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.750A pdb=" N CYS B 934 " --> pdb=" O VAL B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 965 Processing helix chain 'B' and resid 966 through 975 removed outlier: 3.978A pdb=" N GLY B 970 " --> pdb=" O GLY B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 995 Processing helix chain 'B' and resid 1023 through 1041 removed outlier: 3.742A pdb=" N HIS B1041 " --> pdb=" O PHE B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1058 removed outlier: 4.140A pdb=" N MET B1048 " --> pdb=" O ASP B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1070 removed outlier: 3.786A pdb=" N ASP B1068 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1086 Processing helix chain 'C' and resid 40 through 53 removed outlier: 3.911A pdb=" N ASN C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 89 through 104 removed outlier: 4.364A pdb=" N TYR C 93 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.641A pdb=" N GLY C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 removed outlier: 3.561A pdb=" N LEU C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 208 removed outlier: 3.817A pdb=" N ALA C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 363 through 380 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 401 through 418 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 448 through 485 removed outlier: 3.747A pdb=" N GLU C 452 " --> pdb=" O ARG C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 505 Processing helix chain 'C' and resid 507 through 515 Processing helix chain 'C' and resid 515 through 525 removed outlier: 4.670A pdb=" N GLY C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.521A pdb=" N GLU C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 634 Processing helix chain 'C' and resid 640 through 646 removed outlier: 4.246A pdb=" N LYS C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 683 through 708 removed outlier: 4.272A pdb=" N GLN C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 727 Processing helix chain 'C' and resid 735 through 742 Processing helix chain 'C' and resid 748 through 767 Processing helix chain 'C' and resid 778 through 785 Processing helix chain 'C' and resid 787 through 809 Processing helix chain 'C' and resid 812 through 820 removed outlier: 3.553A pdb=" N ASP C 815 " --> pdb=" O HIS C 812 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA C 817 " --> pdb=" O ASP C 814 " (cutoff:3.500A) Proline residue: C 818 - end of helix Processing helix chain 'C' and resid 831 through 849 removed outlier: 4.314A pdb=" N GLY C 836 " --> pdb=" O TYR C 832 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP C 843 " --> pdb=" O ALA C 839 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 846 " --> pdb=" O ILE C 842 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 859 Processing helix chain 'C' and resid 875 through 893 removed outlier: 3.898A pdb=" N ASN C 879 " --> pdb=" O GLU C 875 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 881 " --> pdb=" O ASP C 877 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 884 " --> pdb=" O ASP C 880 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 885 " --> pdb=" O ILE C 881 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 889 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 929 removed outlier: 4.363A pdb=" N GLN C 922 " --> pdb=" O ALA C 918 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 934 Processing helix chain 'C' and resid 941 through 965 removed outlier: 4.178A pdb=" N GLU C 945 " --> pdb=" O SER C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 975 Processing helix chain 'C' and resid 975 through 995 Processing helix chain 'C' and resid 1023 through 1041 removed outlier: 4.087A pdb=" N HIS C1041 " --> pdb=" O PHE C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1058 removed outlier: 3.547A pdb=" N ALA C1045 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU C1046 " --> pdb=" O GLN C1042 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C1048 " --> pdb=" O ASP C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1070 removed outlier: 3.687A pdb=" N ASP C1068 " --> pdb=" O ALA C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1085 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 6.532A pdb=" N PHE A 29 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG A 28 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ALA A 82 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 30 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER A 84 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA A 32 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE A 81 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLY A 114 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 83 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 111 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 136 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLY A 113 " --> pdb=" O TYR A 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 280 removed outlier: 6.433A pdb=" N ILE A 243 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ARG A 277 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 245 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU A 279 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER A 247 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 244 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLU A 310 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 246 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 328 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA A 355 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR A 330 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 532 Processing sheet with id=AA4, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 removed outlier: 3.529A pdb=" N MET A 597 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 624 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS A 621 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A 677 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 623 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR A 679 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR A 625 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 775 through 777 removed outlier: 3.819A pdb=" N GLN A 865 " --> pdb=" O PHE A 824 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 826 " --> pdb=" O GLN A 865 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.325A pdb=" N VAL B 111 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR B 136 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY B 113 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 114 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG B 28 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA B 82 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 30 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N SER B 84 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA B 32 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 57 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 274 through 280 removed outlier: 6.354A pdb=" N ALA B 244 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLU B 310 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 246 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N SER B 312 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 248 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ILE B 314 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N LEU B 212 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N SER B 312 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ILE B 214 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE B 314 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 216 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 217 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 354 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR B 394 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 356 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 527 through 532 Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 544 Processing sheet with id=AB2, first strand: chain 'B' and resid 597 through 598 removed outlier: 3.748A pdb=" N MET B 597 " --> pdb=" O ARG B 622 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 775 through 777 removed outlier: 8.718A pdb=" N HIS B 899 " --> pdb=" O TYR B 862 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 864 " --> pdb=" O HIS B 899 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.402A pdb=" N PHE C 29 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG C 28 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA C 82 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 30 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N SER C 84 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA C 32 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 83 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 134 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.331A pdb=" N ALA C 244 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLU C 310 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 246 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 211 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 329 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLY C 213 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 527 through 532 Processing sheet with id=AB7, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'C' and resid 597 through 598 removed outlier: 3.851A pdb=" N SER C 624 " --> pdb=" O MET C 597 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS C 621 " --> pdb=" O SER C 675 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER C 677 " --> pdb=" O LYS C 621 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 623 " --> pdb=" O SER C 677 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR C 679 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR C 625 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR C 730 " --> pdb=" O THR C 674 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 676 " --> pdb=" O THR C 730 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLN C 732 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N MET C 678 " --> pdb=" O GLN C 732 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER C 773 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 776 through 777 removed outlier: 6.862A pdb=" N ILE C 776 " --> pdb=" O PHE C 823 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N SER C 825 " --> pdb=" O ILE C 776 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 822 " --> pdb=" O HIS C 863 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN C 865 " --> pdb=" O PHE C 822 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE C 824 " --> pdb=" O GLN C 865 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 864 " --> pdb=" O HIS C 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 1267 hydrogen bonds defined for protein. 3678 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: 4.48 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8570 1.34 - 1.46: 3581 1.46 - 1.58: 12745 1.58 - 1.69: 9 1.69 - 1.81: 201 Bond restraints: 25106 Sorted by residual: bond pdb=" CA VAL A 442 " pdb=" C VAL A 442 " ideal model delta sigma weight residual 1.524 1.497 0.028 1.05e-02 9.07e+03 7.11e+00 bond pdb=" C VAL A 555 " pdb=" N LEU A 556 " ideal model delta sigma weight residual 1.327 1.296 0.030 1.39e-02 5.18e+03 4.76e+00 bond pdb=" CA PHE A 359 " pdb=" C PHE A 359 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.20e+00 bond pdb=" C VAL A 442 " pdb=" O VAL A 442 " ideal model delta sigma weight residual 1.240 1.218 0.022 1.26e-02 6.30e+03 2.97e+00 bond pdb=" CA ASN C 938 " pdb=" C ASN C 938 " ideal model delta sigma weight residual 1.519 1.539 -0.020 1.19e-02 7.06e+03 2.85e+00 ... (remaining 25101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 33296 1.75 - 3.51: 630 3.51 - 5.26: 84 5.26 - 7.01: 10 7.01 - 8.77: 2 Bond angle restraints: 34022 Sorted by residual: angle pdb=" C SER C 312 " pdb=" CA SER C 312 " pdb=" CB SER C 312 " ideal model delta sigma weight residual 116.54 109.39 7.15 1.15e+00 7.56e-01 3.86e+01 angle pdb=" C VAL C 442 " pdb=" N PRO C 443 " pdb=" CA PRO C 443 " ideal model delta sigma weight residual 120.38 124.98 -4.60 1.03e+00 9.43e-01 1.99e+01 angle pdb=" C PRO B 443 " pdb=" N PRO B 444 " pdb=" CA PRO B 444 " ideal model delta sigma weight residual 119.84 124.66 -4.82 1.25e+00 6.40e-01 1.49e+01 angle pdb=" N SER C 312 " pdb=" CA SER C 312 " pdb=" C SER C 312 " ideal model delta sigma weight residual 108.31 113.96 -5.65 1.52e+00 4.33e-01 1.38e+01 angle pdb=" N ALA C 351 " pdb=" CA ALA C 351 " pdb=" C ALA C 351 " ideal model delta sigma weight residual 108.34 113.15 -4.81 1.31e+00 5.83e-01 1.35e+01 ... (remaining 34017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 14485 27.90 - 55.80: 561 55.80 - 83.69: 53 83.69 - 111.59: 3 111.59 - 139.49: 2 Dihedral angle restraints: 15104 sinusoidal: 5897 harmonic: 9207 Sorted by residual: dihedral pdb=" O5' GDP C1101 " pdb=" O3A GDP C1101 " pdb=" PA GDP C1101 " pdb=" PB GDP C1101 " ideal model delta sinusoidal sigma weight residual 180.02 40.53 139.49 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O2B GDP A1101 " pdb=" O3A GDP A1101 " pdb=" PB GDP A1101 " pdb=" PA GDP A1101 " ideal model delta sinusoidal sigma weight residual 180.00 48.29 131.71 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2B GDP B1101 " pdb=" O3A GDP B1101 " pdb=" PB GDP B1101 " pdb=" PA GDP B1101 " ideal model delta sinusoidal sigma weight residual 180.00 74.19 105.81 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 15101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2585 0.034 - 0.068: 829 0.068 - 0.101: 283 0.101 - 0.135: 87 0.135 - 0.169: 5 Chirality restraints: 3789 Sorted by residual: chirality pdb=" CA VAL B 442 " pdb=" N VAL B 442 " pdb=" C VAL B 442 " pdb=" CB VAL B 442 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" C1' GDP B1101 " pdb=" O4' GDP B1101 " pdb=" C2' GDP B1101 " pdb=" N9 GDP B1101 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL C 442 " pdb=" N VAL C 442 " pdb=" C VAL C 442 " pdb=" CB VAL C 442 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 3786 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 936 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 937 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 937 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 937 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 939 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C GLN C 939 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN C 939 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 940 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 936 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A 937 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 937 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 937 " 0.026 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 546 2.67 - 3.22: 25668 3.22 - 3.78: 38706 3.78 - 4.34: 47635 4.34 - 4.90: 74869 Nonbonded interactions: 187424 Sorted by model distance: nonbonded pdb=" N ASP C 366 " pdb=" OD1 ASP C 366 " model vdw 2.106 3.120 nonbonded pdb=" OG1 THR C 217 " pdb=" O GLY C 315 " model vdw 2.108 3.040 nonbonded pdb=" OE2 GLU A 738 " pdb=" OG1 THR A 744 " model vdw 2.119 3.040 nonbonded pdb=" N ASP C 402 " pdb=" OD1 ASP C 402 " model vdw 2.120 3.120 nonbonded pdb=" OE2 GLU C 738 " pdb=" OG1 THR C 744 " model vdw 2.137 3.040 ... (remaining 187419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 1101) selection = (chain 'B' and (resid 22 through 357 or (resid 358 and (name N or name CA or nam \ e C or name O or name CB )) or resid 359 through 1101)) selection = (chain 'C' and (resid 22 through 357 or (resid 358 and (name N or name CA or nam \ e C or name O or name CB )) or resid 359 through 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.710 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.003 0.032 25106 Z= 0.187 Angle : 0.609 8.768 34022 Z= 0.362 Chirality : 0.039 0.169 3789 Planarity : 0.004 0.056 4530 Dihedral : 14.057 139.490 9200 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 11.18 % Allowed : 12.30 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.17 (0.15), residues: 3210 helix: 1.01 (0.13), residues: 1635 sheet: 0.08 (0.29), residues: 309 loop : -1.69 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.012 0.001 TYR A 976 PHE 0.018 0.001 PHE C 942 TRP 0.013 0.001 TRP C 929 HIS 0.006 0.001 HIS C 812 Details of bonding type rmsd covalent geometry : bond 0.00334 (25106) covalent geometry : angle 0.60945 (34022) hydrogen bonds : bond 0.16157 ( 1267) hydrogen bonds : angle 6.20562 ( 3678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 1194 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.6847 (mpt-90) cc_final: 0.6647 (mpt-90) REVERT: A 51 GLN cc_start: 0.8531 (tt0) cc_final: 0.8078 (tt0) REVERT: A 75 GLN cc_start: 0.8692 (mt0) cc_final: 0.8309 (mt0) REVERT: A 144 MET cc_start: 0.4878 (OUTLIER) cc_final: 0.4463 (tmm) REVERT: A 242 SER cc_start: 0.7877 (m) cc_final: 0.7556 (t) REVERT: A 243 ILE cc_start: 0.8863 (mt) cc_final: 0.8406 (mp) REVERT: A 263 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8744 (tpp80) REVERT: A 271 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7914 (t70) REVERT: A 274 ILE cc_start: 0.8763 (mp) cc_final: 0.8419 (mp) REVERT: A 296 ILE cc_start: 0.9310 (mm) cc_final: 0.8973 (mt) REVERT: A 314 ILE cc_start: 0.8786 (pt) cc_final: 0.8487 (pt) REVERT: A 335 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 366 ASP cc_start: 0.7993 (m-30) cc_final: 0.6878 (m-30) REVERT: A 376 GLN cc_start: 0.8602 (tt0) cc_final: 0.7879 (tp-100) REVERT: A 422 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.7287 (tp) REVERT: A 452 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8887 (mt-10) REVERT: A 481 HIS cc_start: 0.8698 (t-90) cc_final: 0.8378 (t-170) REVERT: A 515 MET cc_start: 0.9137 (mmt) cc_final: 0.8236 (mmm) REVERT: A 519 MET cc_start: 0.8313 (mmt) cc_final: 0.7955 (mmt) REVERT: A 564 GLU cc_start: 0.7918 (mp0) cc_final: 0.6370 (pm20) REVERT: A 565 ILE cc_start: 0.9369 (mt) cc_final: 0.9086 (pt) REVERT: A 570 MET cc_start: 0.6872 (tpp) cc_final: 0.6527 (tpp) REVERT: A 585 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.5867 (m-10) REVERT: A 610 ARG cc_start: 0.8527 (tpt170) cc_final: 0.8313 (tpt90) REVERT: A 611 PHE cc_start: 0.8014 (m-10) cc_final: 0.7663 (m-80) REVERT: A 623 LEU cc_start: 0.8509 (mt) cc_final: 0.8212 (mp) REVERT: A 624 SER cc_start: 0.6787 (t) cc_final: 0.6479 (m) REVERT: A 688 LEU cc_start: 0.9158 (tp) cc_final: 0.8173 (tp) REVERT: A 699 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8345 (mm-40) REVERT: A 720 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8359 (ttm110) REVERT: A 725 GLN cc_start: 0.8197 (mt0) cc_final: 0.7986 (mm-40) REVERT: A 732 GLN cc_start: 0.8053 (mt0) cc_final: 0.7682 (mt0) REVERT: A 747 PHE cc_start: 0.8639 (m-10) cc_final: 0.8096 (m-10) REVERT: A 750 GLU cc_start: 0.8589 (pm20) cc_final: 0.8179 (pm20) REVERT: A 764 VAL cc_start: 0.9069 (t) cc_final: 0.8738 (t) REVERT: A 766 HIS cc_start: 0.9250 (OUTLIER) cc_final: 0.8616 (m170) REVERT: A 798 ASN cc_start: 0.9048 (m-40) cc_final: 0.8805 (m110) REVERT: A 822 PHE cc_start: 0.9012 (m-80) cc_final: 0.8786 (m-10) REVERT: A 828 MET cc_start: 0.7082 (ttt) cc_final: 0.6352 (ttt) REVERT: A 840 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8311 (mtm-85) REVERT: A 841 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8112 (mtp85) REVERT: A 843 TRP cc_start: 0.8888 (t-100) cc_final: 0.8465 (t-100) REVERT: A 847 MET cc_start: 0.7940 (mmm) cc_final: 0.7476 (mmm) REVERT: A 848 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7653 (tmm-80) REVERT: A 849 ASP cc_start: 0.8925 (p0) cc_final: 0.8635 (p0) REVERT: A 882 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7674 (ptt180) REVERT: A 886 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7307 (mm110) REVERT: A 925 ILE cc_start: 0.8761 (mt) cc_final: 0.8357 (tp) REVERT: A 926 ASN cc_start: 0.8593 (t0) cc_final: 0.8086 (t0) REVERT: A 943 LEU cc_start: 0.8868 (pt) cc_final: 0.8477 (pt) REVERT: A 947 LEU cc_start: 0.7865 (mt) cc_final: 0.7644 (mt) REVERT: A 948 THR cc_start: 0.8872 (m) cc_final: 0.8616 (m) REVERT: A 958 GLU cc_start: 0.7997 (tt0) cc_final: 0.7538 (tp30) REVERT: A 959 PHE cc_start: 0.8865 (m-10) cc_final: 0.8625 (m-80) REVERT: A 962 ILE cc_start: 0.8232 (mm) cc_final: 0.8013 (mm) REVERT: A 973 GLU cc_start: 0.8754 (tt0) cc_final: 0.8252 (tp30) REVERT: A 989 GLU cc_start: 0.8392 (tt0) cc_final: 0.8167 (tp30) REVERT: A 991 LEU cc_start: 0.8823 (mt) cc_final: 0.8444 (tp) REVERT: A 1031 LEU cc_start: 0.9140 (mp) cc_final: 0.8914 (mp) REVERT: A 1063 PHE cc_start: 0.8183 (t80) cc_final: 0.7858 (t80) REVERT: A 1066 LEU cc_start: 0.9389 (mm) cc_final: 0.8950 (mm) REVERT: A 1068 ASP cc_start: 0.9237 (m-30) cc_final: 0.8896 (p0) REVERT: A 1070 VAL cc_start: 0.9274 (m) cc_final: 0.8987 (p) REVERT: A 1079 THR cc_start: 0.8799 (m) cc_final: 0.8513 (m) REVERT: A 1083 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8228 (t80) REVERT: B 151 THR cc_start: 0.9086 (p) cc_final: 0.8806 (p) REVERT: B 183 LEU cc_start: 0.8413 (tp) cc_final: 0.8046 (tp) REVERT: B 230 ILE cc_start: 0.9342 (mt) cc_final: 0.8955 (tp) REVERT: B 243 ILE cc_start: 0.8935 (mt) cc_final: 0.8721 (mm) REVERT: B 246 ILE cc_start: 0.8784 (mt) cc_final: 0.8408 (tp) REVERT: B 259 LEU cc_start: 0.8900 (tt) cc_final: 0.8526 (tt) REVERT: B 288 ILE cc_start: 0.9048 (pt) cc_final: 0.8821 (tp) REVERT: B 292 LEU cc_start: 0.8422 (tp) cc_final: 0.7936 (tp) REVERT: B 300 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8573 (mtpt) REVERT: B 329 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8380 (tp) REVERT: B 331 VAL cc_start: 0.9191 (m) cc_final: 0.8813 (p) REVERT: B 348 LEU cc_start: 0.9323 (mt) cc_final: 0.9101 (mt) REVERT: B 349 ASP cc_start: 0.7976 (t70) cc_final: 0.7686 (t0) REVERT: B 380 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8457 (mp0) REVERT: B 406 MET cc_start: 0.8238 (mtt) cc_final: 0.7786 (mmp) REVERT: B 408 TYR cc_start: 0.8297 (t80) cc_final: 0.8085 (t80) REVERT: B 561 ASP cc_start: 0.6002 (m-30) cc_final: 0.5353 (m-30) REVERT: B 562 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8240 (pt0) REVERT: B 568 TRP cc_start: 0.7909 (t60) cc_final: 0.7057 (t60) REVERT: B 590 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: B 664 TYR cc_start: 0.7158 (m-10) cc_final: 0.6934 (m-10) REVERT: B 667 PHE cc_start: 0.6582 (m-10) cc_final: 0.6369 (m-10) REVERT: B 677 SER cc_start: 0.7621 (p) cc_final: 0.7157 (t) REVERT: B 687 ILE cc_start: 0.8034 (mm) cc_final: 0.7619 (mm) REVERT: B 688 LEU cc_start: 0.9054 (tp) cc_final: 0.8319 (tp) REVERT: B 690 MET cc_start: 0.7858 (mtm) cc_final: 0.7524 (mtm) REVERT: B 697 ASP cc_start: 0.8441 (t0) cc_final: 0.7911 (t0) REVERT: B 704 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7343 (ttm170) REVERT: B 714 ASP cc_start: 0.8436 (m-30) cc_final: 0.8065 (p0) REVERT: B 716 GLU cc_start: 0.8268 (tt0) cc_final: 0.7896 (tm-30) REVERT: B 726 ASN cc_start: 0.8948 (m110) cc_final: 0.8677 (p0) REVERT: B 737 LYS cc_start: 0.9150 (ptmt) cc_final: 0.8676 (pttp) REVERT: B 747 PHE cc_start: 0.7612 (m-10) cc_final: 0.7400 (m-80) REVERT: B 779 TYR cc_start: 0.7331 (t80) cc_final: 0.7113 (t80) REVERT: B 796 LEU cc_start: 0.8880 (mt) cc_final: 0.8175 (mt) REVERT: B 806 TYR cc_start: 0.7179 (m-10) cc_final: 0.6930 (m-10) REVERT: B 814 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8033 (p0) REVERT: B 822 PHE cc_start: 0.7584 (m-80) cc_final: 0.7197 (m-80) REVERT: B 843 TRP cc_start: 0.8812 (t-100) cc_final: 0.8358 (t-100) REVERT: B 855 ASP cc_start: 0.7867 (p0) cc_final: 0.7595 (p0) REVERT: B 864 ILE cc_start: 0.7216 (mm) cc_final: 0.6833 (mm) REVERT: B 870 SER cc_start: 0.8862 (m) cc_final: 0.8517 (t) REVERT: B 946 GLU cc_start: 0.7770 (tp30) cc_final: 0.7313 (tp30) REVERT: B 977 GLN cc_start: 0.9043 (pm20) cc_final: 0.8721 (pm20) REVERT: B 981 ILE cc_start: 0.8998 (mm) cc_final: 0.8737 (tp) REVERT: B 984 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: B 1062 VAL cc_start: 0.9540 (m) cc_final: 0.9240 (p) REVERT: B 1063 PHE cc_start: 0.7391 (t80) cc_final: 0.6728 (t80) REVERT: B 1077 GLN cc_start: 0.8963 (mt0) cc_final: 0.8568 (mp10) REVERT: C 40 ASP cc_start: 0.5118 (OUTLIER) cc_final: 0.4472 (m-30) REVERT: C 53 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7050 (mt0) REVERT: C 66 VAL cc_start: 0.8701 (t) cc_final: 0.7312 (m) REVERT: C 75 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6637 (mt0) REVERT: C 83 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7511 (tp) REVERT: C 136 TYR cc_start: 0.5114 (m-10) cc_final: 0.4121 (m-80) REVERT: C 159 ILE cc_start: 0.8012 (tt) cc_final: 0.7803 (mp) REVERT: C 162 THR cc_start: 0.8189 (p) cc_final: 0.7970 (m) REVERT: C 198 SER cc_start: 0.9357 (m) cc_final: 0.9150 (p) REVERT: C 222 LYS cc_start: 0.7780 (mttt) cc_final: 0.7334 (mttt) REVERT: C 262 ASP cc_start: 0.3633 (OUTLIER) cc_final: 0.3149 (t0) REVERT: C 312 SER cc_start: 0.4865 (OUTLIER) cc_final: 0.4206 (m) REVERT: C 327 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6632 (mm) REVERT: C 344 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.7826 (mttt) REVERT: C 347 MET cc_start: 0.6440 (mmm) cc_final: 0.6102 (tpp) REVERT: C 353 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.4883 (m-80) REVERT: C 371 VAL cc_start: 0.8797 (t) cc_final: 0.8384 (t) REVERT: C 452 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8381 (mp0) REVERT: C 460 TYR cc_start: 0.7192 (t80) cc_final: 0.6491 (t80) REVERT: C 505 LEU cc_start: 0.8382 (tp) cc_final: 0.8141 (tp) REVERT: C 520 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: C 523 TYR cc_start: 0.8207 (m-80) cc_final: 0.7914 (m-10) REVERT: C 561 ASP cc_start: 0.6022 (m-30) cc_final: 0.5232 (m-30) REVERT: C 570 MET cc_start: 0.7752 (tpp) cc_final: 0.7387 (tpt) REVERT: C 632 LEU cc_start: 0.8121 (tt) cc_final: 0.7570 (tt) REVERT: C 675 SER cc_start: 0.7429 (t) cc_final: 0.7200 (p) REVERT: C 687 ILE cc_start: 0.8058 (mt) cc_final: 0.7769 (mm) REVERT: C 703 PHE cc_start: 0.7120 (t80) cc_final: 0.6662 (t80) REVERT: C 756 MET cc_start: 0.8593 (mmm) cc_final: 0.8272 (mmm) REVERT: C 758 ASP cc_start: 0.8088 (t70) cc_final: 0.7801 (t0) REVERT: C 760 GLN cc_start: 0.8454 (tp40) cc_final: 0.8249 (mm-40) REVERT: C 773 SER cc_start: 0.7672 (t) cc_final: 0.7074 (p) REVERT: C 806 TYR cc_start: 0.8304 (m-10) cc_final: 0.8040 (m-10) REVERT: C 825 SER cc_start: 0.7932 (p) cc_final: 0.7116 (t) REVERT: C 837 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7969 (mmm160) REVERT: C 859 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8284 (mppt) REVERT: C 863 HIS cc_start: 0.5329 (OUTLIER) cc_final: 0.3906 (t-90) REVERT: C 875 GLU cc_start: 0.6981 (mt-10) cc_final: 0.5839 (mt-10) REVERT: C 878 PHE cc_start: 0.7792 (m-80) cc_final: 0.6299 (m-80) REVERT: C 944 ILE cc_start: 0.8767 (mt) cc_final: 0.8428 (mt) REVERT: C 945 GLU cc_start: 0.7563 (tt0) cc_final: 0.6191 (tt0) REVERT: C 965 ARG cc_start: 0.6508 (tpt170) cc_final: 0.6107 (tpm170) REVERT: C 969 LEU cc_start: 0.7793 (mp) cc_final: 0.7366 (mp) REVERT: C 1004 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8162 (m) REVERT: C 1005 PHE cc_start: 0.8677 (t80) cc_final: 0.8083 (t80) REVERT: C 1007 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8634 (p0) REVERT: C 1021 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7275 (ttt180) REVERT: C 1060 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7459 (mmt180) REVERT: C 1074 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.6982 (p) REVERT: C 1075 LEU cc_start: 0.7874 (tp) cc_final: 0.7594 (tp) REVERT: C 1091 ARG cc_start: 0.5760 (mmt-90) cc_final: 0.5450 (mmt-90) outliers start: 280 outliers final: 119 residues processed: 1354 average time/residue: 0.1675 time to fit residues: 338.9181 Evaluate side-chains 1110 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 962 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 59 HIS A 75 GLN A 142 GLN A 237 GLN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN A 725 GLN A 732 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 HIS ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A 957 GLN A1028 GLN A1038 HIS ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 104 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN B 237 GLN B 270 ASN B 324 HIS B 378 ASN B 439 ASN B 481 HIS B 699 GLN B 725 GLN B 740 GLN B 743 ASN B 766 HIS B 819 ASN ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 189 ASN C 237 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN C 608 ASN C 725 GLN C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 886 GLN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 GLN C1030 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079240 restraints weight = 76979.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082492 restraints weight = 45482.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084787 restraints weight = 29943.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086403 restraints weight = 21175.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087584 restraints weight = 15909.941| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25106 Z= 0.184 Angle : 0.673 13.755 34022 Z= 0.357 Chirality : 0.045 0.419 3789 Planarity : 0.005 0.070 4530 Dihedral : 6.647 143.793 3573 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.04 (0.15), residues: 3210 helix: 1.14 (0.12), residues: 1641 sheet: -0.15 (0.27), residues: 381 loop : -1.64 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 571 TYR 0.027 0.002 TYR B 580 PHE 0.028 0.002 PHE B1063 TRP 0.010 0.001 TRP C 929 HIS 0.025 0.002 HIS B 899 Details of bonding type rmsd covalent geometry : bond 0.00363 (25106) covalent geometry : angle 0.67349 (34022) hydrogen bonds : bond 0.05103 ( 1267) hydrogen bonds : angle 4.92553 ( 3678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1050 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8368 (m-80) cc_final: 0.8081 (m-80) REVERT: A 39 HIS cc_start: 0.8372 (t70) cc_final: 0.8118 (t70) REVERT: A 45 ILE cc_start: 0.8988 (mt) cc_final: 0.8725 (mt) REVERT: A 75 GLN cc_start: 0.8793 (mt0) cc_final: 0.8457 (mp10) REVERT: A 122 ASP cc_start: 0.8172 (t0) cc_final: 0.7927 (t0) REVERT: A 144 MET cc_start: 0.3326 (ttt) cc_final: 0.2511 (tmm) REVERT: A 149 MET cc_start: 0.7840 (mtt) cc_final: 0.7632 (mtt) REVERT: A 232 ARG cc_start: 0.9025 (mmt90) cc_final: 0.8443 (mmt90) REVERT: A 243 ILE cc_start: 0.9073 (mt) cc_final: 0.8691 (mp) REVERT: A 273 ASN cc_start: 0.8822 (m110) cc_final: 0.7769 (t0) REVERT: A 274 ILE cc_start: 0.8816 (mp) cc_final: 0.8342 (mp) REVERT: A 276 MET cc_start: 0.8169 (tpt) cc_final: 0.6921 (tpt) REVERT: A 292 LEU cc_start: 0.9194 (tp) cc_final: 0.8947 (tt) REVERT: A 332 MET cc_start: 0.8609 (ttm) cc_final: 0.8264 (ttm) REVERT: A 343 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 368 TRP cc_start: 0.8957 (t60) cc_final: 0.8565 (t60) REVERT: A 376 GLN cc_start: 0.8914 (tt0) cc_final: 0.8191 (tp-100) REVERT: A 377 ARG cc_start: 0.8540 (ptp-110) cc_final: 0.8214 (ptp-110) REVERT: A 381 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8097 (tm-30) REVERT: A 388 ASP cc_start: 0.7821 (m-30) cc_final: 0.7594 (m-30) REVERT: A 452 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 500 GLU cc_start: 0.9500 (tm-30) cc_final: 0.8982 (tm-30) REVERT: A 512 LEU cc_start: 0.8897 (tp) cc_final: 0.8618 (tt) REVERT: A 515 MET cc_start: 0.9110 (mmt) cc_final: 0.8680 (mmm) REVERT: A 519 MET cc_start: 0.8765 (mmt) cc_final: 0.8277 (mmm) REVERT: A 555 VAL cc_start: 0.9052 (t) cc_final: 0.8842 (t) REVERT: A 559 PHE cc_start: 0.8443 (m-80) cc_final: 0.8228 (m-80) REVERT: A 561 ASP cc_start: 0.7654 (t70) cc_final: 0.7061 (t70) REVERT: A 562 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 564 GLU cc_start: 0.7778 (mp0) cc_final: 0.7110 (pm20) REVERT: A 570 MET cc_start: 0.7670 (tpp) cc_final: 0.6473 (tpp) REVERT: A 660 MET cc_start: 0.8328 (ttt) cc_final: 0.8017 (ttt) REVERT: A 667 PHE cc_start: 0.8967 (m-80) cc_final: 0.8745 (m-80) REVERT: A 696 ILE cc_start: 0.8790 (mt) cc_final: 0.8483 (mt) REVERT: A 720 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8412 (ttm110) REVERT: A 724 LEU cc_start: 0.9577 (mm) cc_final: 0.9139 (mm) REVERT: A 725 GLN cc_start: 0.8634 (mt0) cc_final: 0.8297 (mm-40) REVERT: A 747 PHE cc_start: 0.8845 (m-10) cc_final: 0.8335 (m-10) REVERT: A 753 LEU cc_start: 0.9161 (mt) cc_final: 0.8861 (mt) REVERT: A 756 MET cc_start: 0.8605 (mmp) cc_final: 0.8199 (mmp) REVERT: A 761 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 789 ILE cc_start: 0.9274 (pt) cc_final: 0.9058 (tt) REVERT: A 794 PHE cc_start: 0.9017 (m-80) cc_final: 0.8807 (m-80) REVERT: A 798 ASN cc_start: 0.9206 (m-40) cc_final: 0.8980 (m110) REVERT: A 804 GLU cc_start: 0.7859 (pt0) cc_final: 0.7463 (pt0) REVERT: A 820 LEU cc_start: 0.8976 (mt) cc_final: 0.8748 (mm) REVERT: A 841 ARG cc_start: 0.9050 (ttm-80) cc_final: 0.8710 (mtp180) REVERT: A 842 ILE cc_start: 0.8982 (mt) cc_final: 0.8659 (tp) REVERT: A 843 TRP cc_start: 0.8801 (t-100) cc_final: 0.8451 (t-100) REVERT: A 847 MET cc_start: 0.8484 (mmm) cc_final: 0.8228 (mmm) REVERT: A 880 ASP cc_start: 0.8586 (m-30) cc_final: 0.8212 (m-30) REVERT: A 882 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7709 (ptt180) REVERT: A 896 ASN cc_start: 0.9053 (m110) cc_final: 0.8743 (m110) REVERT: A 946 GLU cc_start: 0.8386 (tp30) cc_final: 0.8064 (tp30) REVERT: A 958 GLU cc_start: 0.8952 (tt0) cc_final: 0.8509 (tp30) REVERT: A 960 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 1052 LEU cc_start: 0.9010 (mm) cc_final: 0.8799 (mm) REVERT: A 1058 ASP cc_start: 0.7799 (m-30) cc_final: 0.7493 (m-30) REVERT: A 1063 PHE cc_start: 0.8824 (t80) cc_final: 0.8178 (t80) REVERT: A 1068 ASP cc_start: 0.9390 (m-30) cc_final: 0.8852 (p0) REVERT: A 1070 VAL cc_start: 0.9531 (m) cc_final: 0.9329 (p) REVERT: A 1084 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8360 (mm-30) REVERT: B 77 ASP cc_start: 0.8215 (t70) cc_final: 0.7723 (t70) REVERT: B 99 ASP cc_start: 0.7999 (t70) cc_final: 0.7078 (t70) REVERT: B 100 LEU cc_start: 0.7235 (tp) cc_final: 0.7033 (tp) REVERT: B 102 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7640 (ttp80) REVERT: B 183 LEU cc_start: 0.8887 (tp) cc_final: 0.8619 (tp) REVERT: B 276 MET cc_start: 0.7556 (tpt) cc_final: 0.7129 (tpt) REVERT: B 300 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8782 (mtpt) REVERT: B 314 ILE cc_start: 0.9332 (pt) cc_final: 0.9053 (pt) REVERT: B 326 ASP cc_start: 0.8567 (m-30) cc_final: 0.8210 (m-30) REVERT: B 331 VAL cc_start: 0.9031 (m) cc_final: 0.8761 (p) REVERT: B 345 ILE cc_start: 0.9144 (mt) cc_final: 0.8811 (mt) REVERT: B 348 LEU cc_start: 0.9631 (mt) cc_final: 0.9364 (mt) REVERT: B 356 ILE cc_start: 0.8734 (mp) cc_final: 0.8234 (tt) REVERT: B 362 LYS cc_start: 0.8716 (mptt) cc_final: 0.8488 (mptt) REVERT: B 365 GLN cc_start: 0.9190 (mp10) cc_final: 0.8732 (mp10) REVERT: B 377 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.8057 (ttm-80) REVERT: B 389 MET cc_start: 0.8241 (mmp) cc_final: 0.7470 (mmm) REVERT: B 406 MET cc_start: 0.8589 (mtt) cc_final: 0.8235 (mmp) REVERT: B 460 TYR cc_start: 0.8173 (t80) cc_final: 0.7682 (t80) REVERT: B 501 ARG cc_start: 0.7910 (mmt-90) cc_final: 0.7183 (mmt-90) REVERT: B 504 SER cc_start: 0.7971 (t) cc_final: 0.7696 (m) REVERT: B 510 ARG cc_start: 0.9001 (ttp-170) cc_final: 0.8567 (mtm180) REVERT: B 528 TYR cc_start: 0.7922 (t80) cc_final: 0.7534 (t80) REVERT: B 573 ASN cc_start: 0.8146 (t0) cc_final: 0.7573 (m-40) REVERT: B 611 PHE cc_start: 0.7298 (m-10) cc_final: 0.6789 (m-10) REVERT: B 660 MET cc_start: 0.8721 (ttt) cc_final: 0.8348 (ttm) REVERT: B 687 ILE cc_start: 0.8842 (mm) cc_final: 0.8227 (mm) REVERT: B 690 MET cc_start: 0.7922 (mtm) cc_final: 0.7525 (mtm) REVERT: B 697 ASP cc_start: 0.8933 (t0) cc_final: 0.8378 (t0) REVERT: B 701 ASP cc_start: 0.8743 (m-30) cc_final: 0.8276 (m-30) REVERT: B 704 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.7943 (ttt180) REVERT: B 716 GLU cc_start: 0.8682 (tt0) cc_final: 0.8021 (tm-30) REVERT: B 743 ASN cc_start: 0.6628 (t0) cc_final: 0.6371 (t0) REVERT: B 753 LEU cc_start: 0.9286 (mt) cc_final: 0.8981 (mt) REVERT: B 755 VAL cc_start: 0.9577 (t) cc_final: 0.9238 (t) REVERT: B 779 TYR cc_start: 0.8027 (t80) cc_final: 0.7030 (t80) REVERT: B 792 LEU cc_start: 0.9181 (tt) cc_final: 0.8935 (tt) REVERT: B 796 LEU cc_start: 0.9113 (mt) cc_final: 0.8875 (mt) REVERT: B 814 ASP cc_start: 0.8917 (m-30) cc_final: 0.8591 (p0) REVERT: B 822 PHE cc_start: 0.8180 (m-80) cc_final: 0.7801 (m-80) REVERT: B 826 ASN cc_start: 0.8934 (p0) cc_final: 0.8620 (p0) REVERT: B 829 ASP cc_start: 0.7975 (t0) cc_final: 0.7241 (t0) REVERT: B 831 GLU cc_start: 0.8447 (mp0) cc_final: 0.7732 (mp0) REVERT: B 837 ARG cc_start: 0.8767 (mtp85) cc_final: 0.7506 (mtp85) REVERT: B 855 ASP cc_start: 0.8350 (p0) cc_final: 0.7803 (p0) REVERT: B 859 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8409 (mmtt) REVERT: B 882 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.8046 (ptm-80) REVERT: B 889 ILE cc_start: 0.9076 (pt) cc_final: 0.8802 (pt) REVERT: B 936 ASN cc_start: 0.8820 (m110) cc_final: 0.8608 (m110) REVERT: B 946 GLU cc_start: 0.8546 (tp30) cc_final: 0.7813 (tp30) REVERT: B 958 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9033 (tp30) REVERT: B 980 LYS cc_start: 0.9211 (tttp) cc_final: 0.8865 (tttp) REVERT: B 984 GLU cc_start: 0.8944 (pp20) cc_final: 0.8707 (pt0) REVERT: B 1036 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8686 (mt-10) REVERT: B 1054 GLN cc_start: 0.9233 (tm-30) cc_final: 0.9005 (tm-30) REVERT: B 1062 VAL cc_start: 0.9569 (m) cc_final: 0.9176 (p) REVERT: B 1067 MET cc_start: 0.8886 (mmp) cc_final: 0.8484 (mmp) REVERT: C 25 ASN cc_start: 0.6857 (m-40) cc_final: 0.6347 (m-40) REVERT: C 29 PHE cc_start: 0.8859 (m-80) cc_final: 0.8507 (m-80) REVERT: C 66 VAL cc_start: 0.8952 (t) cc_final: 0.8010 (m) REVERT: C 96 TYR cc_start: 0.8620 (t80) cc_final: 0.8402 (t80) REVERT: C 100 LEU cc_start: 0.8576 (mt) cc_final: 0.8221 (mt) REVERT: C 112 PHE cc_start: 0.8246 (m-80) cc_final: 0.7703 (m-80) REVERT: C 136 TYR cc_start: 0.5347 (m-10) cc_final: 0.5072 (m-80) REVERT: C 144 MET cc_start: 0.5259 (ptm) cc_final: 0.4914 (ppp) REVERT: C 162 THR cc_start: 0.8931 (p) cc_final: 0.8396 (m) REVERT: C 227 ASP cc_start: 0.8170 (t0) cc_final: 0.7865 (t0) REVERT: C 230 ILE cc_start: 0.8849 (mt) cc_final: 0.8355 (tt) REVERT: C 347 MET cc_start: 0.7319 (mmm) cc_final: 0.7093 (mmt) REVERT: C 401 ASP cc_start: 0.7957 (t0) cc_final: 0.7611 (t0) REVERT: C 420 MET cc_start: 0.6686 (mpp) cc_final: 0.6216 (mmm) REVERT: C 458 ARG cc_start: 0.8254 (mtm180) cc_final: 0.7909 (mtm180) REVERT: C 477 LEU cc_start: 0.9326 (mt) cc_final: 0.9051 (mt) REVERT: C 505 LEU cc_start: 0.8652 (tp) cc_final: 0.8448 (tp) REVERT: C 520 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8345 (mp10) REVERT: C 532 ILE cc_start: 0.7766 (tp) cc_final: 0.7540 (tt) REVERT: C 570 MET cc_start: 0.8954 (tpp) cc_final: 0.8310 (tpp) REVERT: C 572 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8064 (mt-10) REVERT: C 632 LEU cc_start: 0.8143 (tt) cc_final: 0.7738 (mm) REVERT: C 633 TYR cc_start: 0.8399 (m-10) cc_final: 0.8034 (m-80) REVERT: C 688 LEU cc_start: 0.7844 (tp) cc_final: 0.6880 (tp) REVERT: C 732 GLN cc_start: 0.8918 (mt0) cc_final: 0.8299 (pp30) REVERT: C 750 GLU cc_start: 0.8955 (pm20) cc_final: 0.8656 (pm20) REVERT: C 756 MET cc_start: 0.8943 (mmm) cc_final: 0.8614 (tmm) REVERT: C 763 PHE cc_start: 0.8577 (m-10) cc_final: 0.8355 (m-80) REVERT: C 806 TYR cc_start: 0.9063 (m-10) cc_final: 0.8232 (m-80) REVERT: C 820 LEU cc_start: 0.9118 (mt) cc_final: 0.8890 (mt) REVERT: C 825 SER cc_start: 0.7850 (p) cc_final: 0.7253 (t) REVERT: C 829 ASP cc_start: 0.9105 (m-30) cc_final: 0.8497 (m-30) REVERT: C 837 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8228 (mmm-85) REVERT: C 875 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6738 (mt-10) REVERT: C 878 PHE cc_start: 0.8681 (m-80) cc_final: 0.7121 (m-80) REVERT: C 894 ASN cc_start: 0.8850 (m-40) cc_final: 0.8495 (t0) REVERT: C 896 ASN cc_start: 0.8364 (m110) cc_final: 0.8124 (m-40) REVERT: C 922 GLN cc_start: 0.9243 (tm-30) cc_final: 0.9042 (tm-30) REVERT: C 926 ASN cc_start: 0.8629 (t0) cc_final: 0.8303 (t0) REVERT: C 939 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 944 ILE cc_start: 0.8593 (mt) cc_final: 0.8375 (mt) REVERT: C 945 GLU cc_start: 0.8340 (tt0) cc_final: 0.7706 (tt0) REVERT: C 959 PHE cc_start: 0.8928 (m-10) cc_final: 0.7962 (m-10) REVERT: C 964 GLU cc_start: 0.8481 (tp30) cc_final: 0.8275 (tp30) REVERT: C 965 ARG cc_start: 0.6979 (tpt170) cc_final: 0.6411 (tpm170) REVERT: C 977 GLN cc_start: 0.8869 (mp10) cc_final: 0.8658 (mp10) REVERT: C 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8165 (t80) REVERT: C 1007 ASN cc_start: 0.8745 (m110) cc_final: 0.8380 (p0) REVERT: C 1021 ARG cc_start: 0.7130 (mtt90) cc_final: 0.6618 (ttt-90) REVERT: C 1025 ASP cc_start: 0.7899 (m-30) cc_final: 0.7637 (m-30) REVERT: C 1051 ARG cc_start: 0.7085 (ttt180) cc_final: 0.6764 (ttt180) REVERT: C 1060 ARG cc_start: 0.7699 (mmt180) cc_final: 0.6832 (mmt180) REVERT: C 1063 PHE cc_start: 0.9061 (t80) cc_final: 0.8536 (t80) outliers start: 4 outliers final: 1 residues processed: 1051 average time/residue: 0.1816 time to fit residues: 285.1428 Evaluate side-chains 926 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 925 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 0.0020 chunk 225 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 90 HIS ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN A 766 HIS ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 HIS ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 75 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN B 743 ASN B 760 GLN B 812 HIS B 819 ASN ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074774 restraints weight = 78297.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077810 restraints weight = 46047.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079947 restraints weight = 30257.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081459 restraints weight = 21434.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082565 restraints weight = 16113.354| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25106 Z= 0.294 Angle : 0.765 11.377 34022 Z= 0.413 Chirality : 0.046 0.339 3789 Planarity : 0.007 0.177 4530 Dihedral : 7.176 142.856 3573 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.24 % Allowed : 5.75 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.82 (0.14), residues: 3210 helix: 0.48 (0.12), residues: 1629 sheet: -0.42 (0.28), residues: 345 loop : -1.96 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 263 TYR 0.036 0.003 TYR A 96 PHE 0.026 0.002 PHE B1083 TRP 0.018 0.002 TRP A 929 HIS 0.020 0.003 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00586 (25106) covalent geometry : angle 0.76495 (34022) hydrogen bonds : bond 0.05322 ( 1267) hydrogen bonds : angle 5.34570 ( 3678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 974 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8364 (m-80) cc_final: 0.8085 (m-80) REVERT: A 56 GLU cc_start: 0.7661 (mp0) cc_final: 0.7399 (mp0) REVERT: A 63 ASN cc_start: 0.8805 (t0) cc_final: 0.8585 (t0) REVERT: A 92 GLU cc_start: 0.9077 (mp0) cc_final: 0.8751 (pm20) REVERT: A 97 MET cc_start: 0.8997 (mtm) cc_final: 0.8761 (mtt) REVERT: A 144 MET cc_start: 0.3719 (ttt) cc_final: 0.2620 (tmm) REVERT: A 178 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8363 (mtm180) REVERT: A 222 LYS cc_start: 0.8484 (ptpp) cc_final: 0.7760 (ptpp) REVERT: A 232 ARG cc_start: 0.8979 (mmt90) cc_final: 0.8673 (mmt90) REVERT: A 243 ILE cc_start: 0.9109 (mt) cc_final: 0.8684 (mp) REVERT: A 273 ASN cc_start: 0.8969 (m110) cc_final: 0.7887 (t0) REVERT: A 274 ILE cc_start: 0.8967 (mp) cc_final: 0.8311 (mp) REVERT: A 292 LEU cc_start: 0.9258 (tp) cc_final: 0.9017 (tt) REVERT: A 296 ILE cc_start: 0.9301 (mm) cc_final: 0.9083 (mm) REVERT: A 308 ILE cc_start: 0.8657 (pt) cc_final: 0.8426 (pt) REVERT: A 314 ILE cc_start: 0.8726 (pt) cc_final: 0.8471 (pt) REVERT: A 357 ASN cc_start: 0.9054 (t0) cc_final: 0.8756 (t0) REVERT: A 376 GLN cc_start: 0.9240 (tt0) cc_final: 0.8265 (tp-100) REVERT: A 377 ARG cc_start: 0.8508 (ptp-110) cc_final: 0.8295 (ptp-110) REVERT: A 381 GLN cc_start: 0.8938 (tp-100) cc_final: 0.7835 (tm-30) REVERT: A 388 ASP cc_start: 0.7641 (m-30) cc_final: 0.7394 (m-30) REVERT: A 500 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9031 (tm-30) REVERT: A 512 LEU cc_start: 0.8997 (tp) cc_final: 0.8733 (tt) REVERT: A 515 MET cc_start: 0.8778 (mmt) cc_final: 0.8195 (mmm) REVERT: A 519 MET cc_start: 0.9015 (mmt) cc_final: 0.8452 (mmp) REVERT: A 559 PHE cc_start: 0.8345 (m-80) cc_final: 0.7950 (m-80) REVERT: A 564 GLU cc_start: 0.8034 (mp0) cc_final: 0.7696 (mp0) REVERT: A 570 MET cc_start: 0.7793 (tpp) cc_final: 0.6628 (tpp) REVERT: A 635 GLU cc_start: 0.8244 (mp0) cc_final: 0.7881 (mp0) REVERT: A 654 ILE cc_start: 0.8994 (pt) cc_final: 0.8637 (pt) REVERT: A 667 PHE cc_start: 0.9083 (m-80) cc_final: 0.8832 (m-80) REVERT: A 690 MET cc_start: 0.9106 (mtm) cc_final: 0.8809 (mtm) REVERT: A 720 ARG cc_start: 0.8783 (mtp-110) cc_final: 0.8179 (ttm110) REVERT: A 724 LEU cc_start: 0.9441 (mm) cc_final: 0.9145 (mm) REVERT: A 725 GLN cc_start: 0.8664 (mt0) cc_final: 0.8402 (mt0) REVERT: A 747 PHE cc_start: 0.8909 (m-10) cc_final: 0.8508 (m-10) REVERT: A 750 GLU cc_start: 0.9178 (pm20) cc_final: 0.8696 (pm20) REVERT: A 753 LEU cc_start: 0.9190 (mt) cc_final: 0.8986 (mt) REVERT: A 756 MET cc_start: 0.8529 (mmp) cc_final: 0.8118 (mmp) REVERT: A 761 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 800 PHE cc_start: 0.9086 (m-80) cc_final: 0.8871 (m-80) REVERT: A 804 GLU cc_start: 0.7987 (pt0) cc_final: 0.7735 (pt0) REVERT: A 824 PHE cc_start: 0.9155 (p90) cc_final: 0.8566 (p90) REVERT: A 837 ARG cc_start: 0.8615 (mtp85) cc_final: 0.7993 (mtp85) REVERT: A 842 ILE cc_start: 0.9107 (mt) cc_final: 0.8746 (tp) REVERT: A 843 TRP cc_start: 0.8755 (t-100) cc_final: 0.8275 (t-100) REVERT: A 847 MET cc_start: 0.8570 (mmm) cc_final: 0.8176 (mmt) REVERT: A 880 ASP cc_start: 0.8425 (m-30) cc_final: 0.8087 (m-30) REVERT: A 882 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.7869 (ptt180) REVERT: A 898 LEU cc_start: 0.8901 (tp) cc_final: 0.8557 (tt) REVERT: A 917 ARG cc_start: 0.9038 (ptm160) cc_final: 0.8750 (ptm160) REVERT: A 939 GLN cc_start: 0.8605 (tt0) cc_final: 0.8349 (tt0) REVERT: A 955 VAL cc_start: 0.9239 (t) cc_final: 0.8991 (p) REVERT: A 959 PHE cc_start: 0.9269 (m-80) cc_final: 0.8898 (m-80) REVERT: A 1000 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 1058 ASP cc_start: 0.8250 (m-30) cc_final: 0.7649 (m-30) REVERT: A 1066 LEU cc_start: 0.9600 (mm) cc_final: 0.9375 (mm) REVERT: A 1084 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 68 GLU cc_start: 0.7582 (tp30) cc_final: 0.7328 (tp30) REVERT: B 75 GLN cc_start: 0.8864 (tt0) cc_final: 0.8637 (tt0) REVERT: B 77 ASP cc_start: 0.8264 (t70) cc_final: 0.7725 (t70) REVERT: B 127 LEU cc_start: 0.8992 (mt) cc_final: 0.8704 (mt) REVERT: B 149 MET cc_start: 0.7964 (ppp) cc_final: 0.7607 (ppp) REVERT: B 152 ASP cc_start: 0.8821 (m-30) cc_final: 0.8569 (m-30) REVERT: B 183 LEU cc_start: 0.8922 (tp) cc_final: 0.8665 (tp) REVERT: B 228 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8603 (mm-30) REVERT: B 300 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8740 (mtpt) REVERT: B 329 LEU cc_start: 0.9082 (tp) cc_final: 0.8861 (tp) REVERT: B 331 VAL cc_start: 0.8979 (m) cc_final: 0.8519 (p) REVERT: B 345 ILE cc_start: 0.9075 (mt) cc_final: 0.8660 (mt) REVERT: B 348 LEU cc_start: 0.9676 (mt) cc_final: 0.9373 (mt) REVERT: B 356 ILE cc_start: 0.8609 (mp) cc_final: 0.8183 (tt) REVERT: B 362 LYS cc_start: 0.8886 (mptt) cc_final: 0.8656 (mptt) REVERT: B 365 GLN cc_start: 0.9191 (mp10) cc_final: 0.8931 (mp10) REVERT: B 377 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7549 (ttm-80) REVERT: B 389 MET cc_start: 0.8287 (mmp) cc_final: 0.7655 (mmp) REVERT: B 448 ARG cc_start: 0.8466 (mtt90) cc_final: 0.8026 (mtt90) REVERT: B 460 TYR cc_start: 0.8295 (t80) cc_final: 0.7621 (t80) REVERT: B 501 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7033 (mmt-90) REVERT: B 504 SER cc_start: 0.7881 (t) cc_final: 0.7563 (m) REVERT: B 528 TYR cc_start: 0.7868 (t80) cc_final: 0.7273 (t80) REVERT: B 567 LYS cc_start: 0.8697 (tttm) cc_final: 0.8433 (tttm) REVERT: B 611 PHE cc_start: 0.7405 (m-10) cc_final: 0.6903 (m-10) REVERT: B 618 MET cc_start: 0.8279 (mmm) cc_final: 0.8066 (ttt) REVERT: B 621 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7115 (mmpt) REVERT: B 660 MET cc_start: 0.8804 (ttt) cc_final: 0.8556 (ttm) REVERT: B 663 LEU cc_start: 0.9381 (mt) cc_final: 0.9125 (mt) REVERT: B 687 ILE cc_start: 0.8948 (mm) cc_final: 0.8358 (mm) REVERT: B 688 LEU cc_start: 0.9287 (tp) cc_final: 0.8752 (tp) REVERT: B 690 MET cc_start: 0.7753 (mtm) cc_final: 0.7471 (mtm) REVERT: B 692 MET cc_start: 0.8719 (mmp) cc_final: 0.8435 (mmp) REVERT: B 704 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.8007 (ttt180) REVERT: B 716 GLU cc_start: 0.8818 (tt0) cc_final: 0.8297 (tm-30) REVERT: B 738 GLU cc_start: 0.7922 (tp30) cc_final: 0.7261 (tp30) REVERT: B 743 ASN cc_start: 0.7240 (t0) cc_final: 0.7025 (t0) REVERT: B 753 LEU cc_start: 0.9327 (mt) cc_final: 0.9005 (mt) REVERT: B 756 MET cc_start: 0.9239 (mmp) cc_final: 0.9016 (mmp) REVERT: B 779 TYR cc_start: 0.7981 (t80) cc_final: 0.7176 (t80) REVERT: B 792 LEU cc_start: 0.9196 (tt) cc_final: 0.8903 (tt) REVERT: B 796 LEU cc_start: 0.9339 (mt) cc_final: 0.8821 (mt) REVERT: B 800 PHE cc_start: 0.8773 (m-80) cc_final: 0.8378 (m-80) REVERT: B 814 ASP cc_start: 0.8975 (m-30) cc_final: 0.8638 (p0) REVERT: B 815 ASP cc_start: 0.8703 (m-30) cc_final: 0.8377 (m-30) REVERT: B 822 PHE cc_start: 0.8113 (m-80) cc_final: 0.7861 (m-80) REVERT: B 826 ASN cc_start: 0.8823 (p0) cc_final: 0.8534 (p0) REVERT: B 831 GLU cc_start: 0.8565 (mp0) cc_final: 0.8039 (mp0) REVERT: B 855 ASP cc_start: 0.8248 (p0) cc_final: 0.7699 (p0) REVERT: B 858 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 859 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8364 (mtmt) REVERT: B 889 ILE cc_start: 0.9087 (pt) cc_final: 0.8883 (pt) REVERT: B 936 ASN cc_start: 0.8966 (m-40) cc_final: 0.8758 (m110) REVERT: B 946 GLU cc_start: 0.8678 (tp30) cc_final: 0.7813 (tp30) REVERT: B 958 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9053 (tp30) REVERT: B 977 GLN cc_start: 0.8996 (pm20) cc_final: 0.8596 (pm20) REVERT: B 1036 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 1054 GLN cc_start: 0.9238 (tm-30) cc_final: 0.9025 (tm-30) REVERT: B 1062 VAL cc_start: 0.9628 (m) cc_final: 0.9260 (p) REVERT: B 1067 MET cc_start: 0.8928 (mmp) cc_final: 0.8445 (mmp) REVERT: C 29 PHE cc_start: 0.8928 (m-80) cc_final: 0.8433 (m-10) REVERT: C 64 ARG cc_start: 0.7911 (mmm160) cc_final: 0.6207 (mmm160) REVERT: C 100 LEU cc_start: 0.8251 (mt) cc_final: 0.7642 (mt) REVERT: C 112 PHE cc_start: 0.8321 (m-80) cc_final: 0.7982 (m-80) REVERT: C 161 LEU cc_start: 0.8646 (mp) cc_final: 0.8068 (tp) REVERT: C 227 ASP cc_start: 0.8238 (t0) cc_final: 0.8031 (t0) REVERT: C 389 MET cc_start: 0.8650 (tpt) cc_final: 0.8189 (tpt) REVERT: C 401 ASP cc_start: 0.7946 (t0) cc_final: 0.7508 (t0) REVERT: C 450 LEU cc_start: 0.8954 (tp) cc_final: 0.8742 (tp) REVERT: C 452 GLU cc_start: 0.8848 (mp0) cc_final: 0.8596 (mp0) REVERT: C 476 GLN cc_start: 0.9304 (mp10) cc_final: 0.9048 (mt0) REVERT: C 477 LEU cc_start: 0.9381 (mt) cc_final: 0.9122 (mt) REVERT: C 497 LEU cc_start: 0.8871 (mt) cc_final: 0.8355 (mm) REVERT: C 500 GLU cc_start: 0.9441 (tt0) cc_final: 0.9235 (mt-10) REVERT: C 502 ASP cc_start: 0.8942 (m-30) cc_final: 0.8731 (t70) REVERT: C 520 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8224 (mm-40) REVERT: C 570 MET cc_start: 0.9087 (tpp) cc_final: 0.8551 (tpp) REVERT: C 572 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 588 LYS cc_start: 0.9004 (tptp) cc_final: 0.8788 (tptt) REVERT: C 633 TYR cc_start: 0.8281 (m-10) cc_final: 0.7902 (m-80) REVERT: C 662 VAL cc_start: 0.9247 (p) cc_final: 0.9000 (p) REVERT: C 665 ASP cc_start: 0.8725 (p0) cc_final: 0.8435 (p0) REVERT: C 756 MET cc_start: 0.8982 (mmm) cc_final: 0.8473 (tmm) REVERT: C 763 PHE cc_start: 0.8729 (m-10) cc_final: 0.8418 (m-80) REVERT: C 806 TYR cc_start: 0.8234 (m-10) cc_final: 0.7206 (m-80) REVERT: C 826 ASN cc_start: 0.8148 (m110) cc_final: 0.7611 (m110) REVERT: C 835 LEU cc_start: 0.8779 (tp) cc_final: 0.8545 (tp) REVERT: C 861 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8672 (mtmt) REVERT: C 875 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6735 (mt-10) REVERT: C 878 PHE cc_start: 0.8728 (m-80) cc_final: 0.6881 (m-80) REVERT: C 885 LEU cc_start: 0.9357 (tp) cc_final: 0.9145 (tp) REVERT: C 894 ASN cc_start: 0.8831 (m-40) cc_final: 0.8518 (t0) REVERT: C 922 GLN cc_start: 0.9204 (tm-30) cc_final: 0.9000 (tm-30) REVERT: C 924 ILE cc_start: 0.8569 (mm) cc_final: 0.8288 (mm) REVERT: C 926 ASN cc_start: 0.8980 (t0) cc_final: 0.8544 (t0) REVERT: C 944 ILE cc_start: 0.8697 (mt) cc_final: 0.8455 (mt) REVERT: C 945 GLU cc_start: 0.8410 (tt0) cc_final: 0.7738 (tt0) REVERT: C 949 ASP cc_start: 0.9010 (m-30) cc_final: 0.8767 (m-30) REVERT: C 955 VAL cc_start: 0.9096 (t) cc_final: 0.8760 (t) REVERT: C 959 PHE cc_start: 0.8870 (m-10) cc_final: 0.8443 (m-80) REVERT: C 962 ILE cc_start: 0.9084 (mm) cc_final: 0.8865 (mm) REVERT: C 964 GLU cc_start: 0.8565 (tp30) cc_final: 0.8253 (tp30) REVERT: C 965 ARG cc_start: 0.6106 (tpt170) cc_final: 0.5556 (tpm170) REVERT: C 977 GLN cc_start: 0.8897 (mp10) cc_final: 0.8587 (mp10) REVERT: C 978 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8510 (ttt90) REVERT: C 989 GLU cc_start: 0.8768 (tp30) cc_final: 0.8344 (tp30) REVERT: C 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8297 (t80) REVERT: C 1007 ASN cc_start: 0.8890 (m110) cc_final: 0.8402 (p0) REVERT: C 1021 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6709 (ttt-90) REVERT: C 1025 ASP cc_start: 0.7953 (m-30) cc_final: 0.7673 (m-30) REVERT: C 1051 ARG cc_start: 0.7365 (ttt180) cc_final: 0.6685 (ttt180) REVERT: C 1060 ARG cc_start: 0.7898 (mmt180) cc_final: 0.7022 (mmt180) outliers start: 6 outliers final: 2 residues processed: 977 average time/residue: 0.1707 time to fit residues: 250.1163 Evaluate side-chains 891 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 888 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 33 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 251 optimal weight: 0.3980 chunk 148 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 409 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN A1088 GLN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 378 ASN B 409 GLN B 819 ASN B 858 GLN ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 520 GLN C 725 GLN C 858 GLN ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 HIS C 896 ASN ** C 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1015 GLN C1080 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080102 restraints weight = 76407.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083227 restraints weight = 45377.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085409 restraints weight = 30026.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086961 restraints weight = 21372.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088107 restraints weight = 16161.858| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25106 Z= 0.136 Angle : 0.635 10.604 34022 Z= 0.333 Chirality : 0.043 0.261 3789 Planarity : 0.005 0.090 4530 Dihedral : 6.647 141.339 3573 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.17 (0.15), residues: 3210 helix: 1.02 (0.12), residues: 1623 sheet: -0.24 (0.28), residues: 345 loop : -1.60 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 433 TYR 0.027 0.002 TYR A 762 PHE 0.026 0.002 PHE A1063 TRP 0.010 0.001 TRP C 516 HIS 0.009 0.001 HIS B 899 Details of bonding type rmsd covalent geometry : bond 0.00288 (25106) covalent geometry : angle 0.63494 (34022) hydrogen bonds : bond 0.04417 ( 1267) hydrogen bonds : angle 4.57692 ( 3678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 986 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7511 (mp0) cc_final: 0.7201 (mp0) REVERT: A 75 GLN cc_start: 0.8971 (mt0) cc_final: 0.8486 (mp10) REVERT: A 92 GLU cc_start: 0.9048 (mp0) cc_final: 0.8618 (pm20) REVERT: A 108 HIS cc_start: 0.8789 (p-80) cc_final: 0.8520 (m-70) REVERT: A 144 MET cc_start: 0.3505 (ttt) cc_final: 0.2435 (tmm) REVERT: A 164 TYR cc_start: 0.7355 (t80) cc_final: 0.6609 (t80) REVERT: A 222 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7594 (ptpp) REVERT: A 232 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8589 (mmt90) REVERT: A 241 LEU cc_start: 0.9100 (mt) cc_final: 0.8381 (mm) REVERT: A 243 ILE cc_start: 0.9012 (mt) cc_final: 0.8736 (mp) REVERT: A 260 LEU cc_start: 0.9038 (mp) cc_final: 0.8807 (mp) REVERT: A 273 ASN cc_start: 0.8772 (m110) cc_final: 0.7896 (t0) REVERT: A 296 ILE cc_start: 0.9290 (mm) cc_final: 0.9030 (mt) REVERT: A 306 LEU cc_start: 0.9237 (tp) cc_final: 0.8863 (mm) REVERT: A 332 MET cc_start: 0.8446 (ttm) cc_final: 0.8142 (tpp) REVERT: A 346 ASP cc_start: 0.8282 (m-30) cc_final: 0.8069 (m-30) REVERT: A 357 ASN cc_start: 0.8686 (t0) cc_final: 0.8425 (t0) REVERT: A 368 TRP cc_start: 0.9044 (t60) cc_final: 0.8557 (t60) REVERT: A 376 GLN cc_start: 0.9145 (tt0) cc_final: 0.8264 (tp-100) REVERT: A 381 GLN cc_start: 0.8854 (tp-100) cc_final: 0.7913 (tm-30) REVERT: A 388 ASP cc_start: 0.7747 (m-30) cc_final: 0.7531 (m-30) REVERT: A 406 MET cc_start: 0.8411 (mtp) cc_final: 0.7858 (mtp) REVERT: A 470 LEU cc_start: 0.9161 (mt) cc_final: 0.8873 (mt) REVERT: A 481 HIS cc_start: 0.8907 (t70) cc_final: 0.8271 (t70) REVERT: A 482 ASP cc_start: 0.8920 (m-30) cc_final: 0.8652 (m-30) REVERT: A 500 GLU cc_start: 0.9506 (tm-30) cc_final: 0.8968 (tm-30) REVERT: A 513 LEU cc_start: 0.9352 (tp) cc_final: 0.8425 (tp) REVERT: A 519 MET cc_start: 0.8545 (mmt) cc_final: 0.8121 (mmp) REVERT: A 520 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7997 (mm110) REVERT: A 556 LEU cc_start: 0.9296 (mt) cc_final: 0.9068 (mt) REVERT: A 588 LYS cc_start: 0.9371 (ttmt) cc_final: 0.9016 (ttpp) REVERT: A 635 GLU cc_start: 0.8268 (mp0) cc_final: 0.8029 (mp0) REVERT: A 654 ILE cc_start: 0.8939 (pt) cc_final: 0.8691 (pt) REVERT: A 657 LEU cc_start: 0.8647 (tp) cc_final: 0.8247 (tp) REVERT: A 660 MET cc_start: 0.8387 (ttt) cc_final: 0.7890 (ttt) REVERT: A 667 PHE cc_start: 0.8959 (m-80) cc_final: 0.8746 (m-80) REVERT: A 688 LEU cc_start: 0.9362 (tp) cc_final: 0.9104 (pp) REVERT: A 690 MET cc_start: 0.8928 (mtm) cc_final: 0.8662 (ptp) REVERT: A 720 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8316 (ttm110) REVERT: A 724 LEU cc_start: 0.9477 (mm) cc_final: 0.9128 (mm) REVERT: A 725 GLN cc_start: 0.8598 (mt0) cc_final: 0.8253 (mm-40) REVERT: A 735 ILE cc_start: 0.9334 (mm) cc_final: 0.9090 (mm) REVERT: A 747 PHE cc_start: 0.8734 (m-80) cc_final: 0.8277 (m-10) REVERT: A 750 GLU cc_start: 0.8952 (pm20) cc_final: 0.8536 (pm20) REVERT: A 753 LEU cc_start: 0.9160 (mt) cc_final: 0.8910 (mt) REVERT: A 756 MET cc_start: 0.8429 (mmp) cc_final: 0.7958 (mmp) REVERT: A 761 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 763 PHE cc_start: 0.9040 (m-10) cc_final: 0.8838 (m-10) REVERT: A 798 ASN cc_start: 0.9341 (m-40) cc_final: 0.9096 (m110) REVERT: A 804 GLU cc_start: 0.7832 (pt0) cc_final: 0.7531 (pt0) REVERT: A 824 PHE cc_start: 0.9129 (p90) cc_final: 0.8672 (p90) REVERT: A 841 ARG cc_start: 0.8994 (ttm170) cc_final: 0.8066 (ttt180) REVERT: A 842 ILE cc_start: 0.9028 (mt) cc_final: 0.8729 (tp) REVERT: A 843 TRP cc_start: 0.8632 (t-100) cc_final: 0.8267 (t-100) REVERT: A 847 MET cc_start: 0.8261 (mmm) cc_final: 0.7900 (mmt) REVERT: A 880 ASP cc_start: 0.8368 (m-30) cc_final: 0.8060 (m-30) REVERT: A 896 ASN cc_start: 0.8976 (m110) cc_final: 0.8692 (m110) REVERT: A 925 ILE cc_start: 0.8687 (mm) cc_final: 0.8324 (tt) REVERT: A 958 GLU cc_start: 0.8830 (tt0) cc_final: 0.8318 (tp30) REVERT: A 962 ILE cc_start: 0.9033 (mm) cc_final: 0.8035 (mm) REVERT: A 976 TYR cc_start: 0.8059 (t80) cc_final: 0.7754 (t80) REVERT: A 1066 LEU cc_start: 0.9559 (mm) cc_final: 0.9335 (mm) REVERT: A 1084 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 1093 MET cc_start: 0.8297 (tpt) cc_final: 0.7991 (tpt) REVERT: B 75 GLN cc_start: 0.8905 (tt0) cc_final: 0.8609 (tt0) REVERT: B 77 ASP cc_start: 0.8235 (t70) cc_final: 0.7937 (t70) REVERT: B 94 PHE cc_start: 0.9272 (m-80) cc_final: 0.9017 (m-10) REVERT: B 95 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8726 (mtmm) REVERT: B 127 LEU cc_start: 0.8795 (mt) cc_final: 0.8511 (mt) REVERT: B 152 ASP cc_start: 0.8755 (m-30) cc_final: 0.8552 (m-30) REVERT: B 183 LEU cc_start: 0.8822 (tp) cc_final: 0.8557 (tp) REVERT: B 189 ASN cc_start: 0.7489 (t0) cc_final: 0.7166 (p0) REVERT: B 200 LEU cc_start: 0.9095 (mm) cc_final: 0.8780 (tp) REVERT: B 227 ASP cc_start: 0.8270 (t70) cc_final: 0.8065 (t70) REVERT: B 275 PHE cc_start: 0.8264 (t80) cc_final: 0.8058 (t80) REVERT: B 300 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8712 (mtpt) REVERT: B 314 ILE cc_start: 0.9334 (pt) cc_final: 0.9068 (pt) REVERT: B 331 VAL cc_start: 0.8995 (m) cc_final: 0.8704 (p) REVERT: B 345 ILE cc_start: 0.8840 (mt) cc_final: 0.8373 (mt) REVERT: B 348 LEU cc_start: 0.9568 (mt) cc_final: 0.9201 (mt) REVERT: B 356 ILE cc_start: 0.8766 (mp) cc_final: 0.8355 (tt) REVERT: B 358 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7700 (mttt) REVERT: B 360 ASP cc_start: 0.8485 (t0) cc_final: 0.7346 (p0) REVERT: B 362 LYS cc_start: 0.8837 (mptt) cc_final: 0.8575 (mptt) REVERT: B 365 GLN cc_start: 0.9170 (mp10) cc_final: 0.8866 (mp10) REVERT: B 389 MET cc_start: 0.8393 (mmp) cc_final: 0.7675 (mmm) REVERT: B 406 MET cc_start: 0.8550 (mtm) cc_final: 0.8316 (mmp) REVERT: B 448 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7926 (mtt90) REVERT: B 460 TYR cc_start: 0.8137 (t80) cc_final: 0.7578 (t80) REVERT: B 504 SER cc_start: 0.7746 (t) cc_final: 0.7509 (m) REVERT: B 512 LEU cc_start: 0.9536 (mm) cc_final: 0.9138 (pp) REVERT: B 528 TYR cc_start: 0.7643 (t80) cc_final: 0.7078 (t80) REVERT: B 597 MET cc_start: 0.8276 (tmm) cc_final: 0.8026 (tmm) REVERT: B 611 PHE cc_start: 0.7258 (m-10) cc_final: 0.6663 (m-10) REVERT: B 621 LYS cc_start: 0.7693 (mmpt) cc_final: 0.6943 (mmpt) REVERT: B 660 MET cc_start: 0.8638 (ttt) cc_final: 0.8392 (ttt) REVERT: B 663 LEU cc_start: 0.9306 (mt) cc_final: 0.9040 (mt) REVERT: B 687 ILE cc_start: 0.8923 (mm) cc_final: 0.8271 (mm) REVERT: B 688 LEU cc_start: 0.9244 (tp) cc_final: 0.8537 (tp) REVERT: B 690 MET cc_start: 0.7710 (mtm) cc_final: 0.7393 (mtm) REVERT: B 692 MET cc_start: 0.8660 (mmp) cc_final: 0.8445 (mmp) REVERT: B 697 ASP cc_start: 0.8728 (m-30) cc_final: 0.8455 (m-30) REVERT: B 704 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7923 (ttt180) REVERT: B 716 GLU cc_start: 0.8723 (tt0) cc_final: 0.8204 (tm-30) REVERT: B 738 GLU cc_start: 0.7707 (tp30) cc_final: 0.7050 (tp30) REVERT: B 743 ASN cc_start: 0.6970 (t0) cc_final: 0.6567 (t0) REVERT: B 753 LEU cc_start: 0.8960 (mt) cc_final: 0.8751 (mt) REVERT: B 755 VAL cc_start: 0.9528 (t) cc_final: 0.9245 (t) REVERT: B 779 TYR cc_start: 0.7868 (t80) cc_final: 0.7064 (t80) REVERT: B 789 ILE cc_start: 0.8490 (pt) cc_final: 0.7794 (pt) REVERT: B 796 LEU cc_start: 0.9219 (mt) cc_final: 0.8592 (mt) REVERT: B 800 PHE cc_start: 0.8758 (m-80) cc_final: 0.8335 (m-80) REVERT: B 814 ASP cc_start: 0.8918 (m-30) cc_final: 0.8571 (p0) REVERT: B 822 PHE cc_start: 0.8011 (m-80) cc_final: 0.7750 (m-80) REVERT: B 826 ASN cc_start: 0.8675 (p0) cc_final: 0.8428 (p0) REVERT: B 828 MET cc_start: 0.7785 (tmm) cc_final: 0.7243 (tpt) REVERT: B 829 ASP cc_start: 0.8044 (t0) cc_final: 0.7571 (t0) REVERT: B 831 GLU cc_start: 0.8732 (mp0) cc_final: 0.8432 (mp0) REVERT: B 837 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8515 (mtp85) REVERT: B 841 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7742 (ptm160) REVERT: B 848 ARG cc_start: 0.8994 (tmt170) cc_final: 0.8263 (tpp80) REVERT: B 858 GLN cc_start: 0.8824 (tm130) cc_final: 0.7635 (tm-30) REVERT: B 859 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8248 (mtmt) REVERT: B 889 ILE cc_start: 0.9056 (pt) cc_final: 0.8835 (pt) REVERT: B 946 GLU cc_start: 0.8673 (tp30) cc_final: 0.7986 (tp30) REVERT: B 958 GLU cc_start: 0.9436 (mm-30) cc_final: 0.8980 (tp30) REVERT: B 981 ILE cc_start: 0.9552 (mm) cc_final: 0.9186 (tp) REVERT: B 984 GLU cc_start: 0.9071 (pt0) cc_final: 0.8559 (pp20) REVERT: B 1036 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8684 (mt-10) REVERT: B 1054 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8788 (tm-30) REVERT: B 1066 LEU cc_start: 0.9302 (mm) cc_final: 0.9081 (mm) REVERT: B 1067 MET cc_start: 0.8781 (mmp) cc_final: 0.8189 (mmp) REVERT: B 1078 ILE cc_start: 0.9494 (tt) cc_final: 0.9273 (tp) REVERT: C 29 PHE cc_start: 0.8520 (m-80) cc_final: 0.8081 (m-80) REVERT: C 64 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7167 (mmm160) REVERT: C 66 VAL cc_start: 0.8928 (t) cc_final: 0.8165 (m) REVERT: C 103 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8283 (pt0) REVERT: C 112 PHE cc_start: 0.8211 (m-80) cc_final: 0.7798 (m-80) REVERT: C 161 LEU cc_start: 0.8632 (mp) cc_final: 0.8043 (tp) REVERT: C 227 ASP cc_start: 0.8372 (t0) cc_final: 0.7877 (t0) REVERT: C 230 ILE cc_start: 0.8850 (mm) cc_final: 0.8276 (tt) REVERT: C 326 ASP cc_start: 0.4780 (t0) cc_final: 0.4262 (p0) REVERT: C 342 LEU cc_start: 0.8791 (tp) cc_final: 0.8545 (mp) REVERT: C 347 MET cc_start: 0.6866 (mmt) cc_final: 0.6385 (mmt) REVERT: C 376 GLN cc_start: 0.7856 (tt0) cc_final: 0.7559 (tm-30) REVERT: C 389 MET cc_start: 0.8451 (tpt) cc_final: 0.8140 (tpt) REVERT: C 401 ASP cc_start: 0.7829 (t0) cc_final: 0.7569 (t0) REVERT: C 450 LEU cc_start: 0.8821 (tp) cc_final: 0.8574 (tp) REVERT: C 520 GLN cc_start: 0.8987 (mm110) cc_final: 0.8142 (mm110) REVERT: C 569 LEU cc_start: 0.8475 (pp) cc_final: 0.8196 (pp) REVERT: C 570 MET cc_start: 0.9064 (tpp) cc_final: 0.8536 (tpp) REVERT: C 572 GLU cc_start: 0.8734 (mt-10) cc_final: 0.7977 (mt-10) REVERT: C 633 TYR cc_start: 0.8102 (m-10) cc_final: 0.7737 (m-80) REVERT: C 662 VAL cc_start: 0.9283 (p) cc_final: 0.9029 (p) REVERT: C 702 ARG cc_start: 0.8301 (ppt170) cc_final: 0.7905 (ttp80) REVERT: C 756 MET cc_start: 0.8974 (mmm) cc_final: 0.8271 (tmm) REVERT: C 763 PHE cc_start: 0.8571 (m-10) cc_final: 0.8297 (m-80) REVERT: C 791 GLN cc_start: 0.8946 (tt0) cc_final: 0.8636 (tt0) REVERT: C 806 TYR cc_start: 0.8029 (m-10) cc_final: 0.7027 (m-80) REVERT: C 826 ASN cc_start: 0.7167 (m110) cc_final: 0.6960 (m110) REVERT: C 835 LEU cc_start: 0.8423 (tp) cc_final: 0.8215 (tp) REVERT: C 841 ARG cc_start: 0.8581 (ttm170) cc_final: 0.8293 (ttm170) REVERT: C 875 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6722 (mt-10) REVERT: C 878 PHE cc_start: 0.8731 (m-80) cc_final: 0.7188 (m-80) REVERT: C 894 ASN cc_start: 0.8906 (m-40) cc_final: 0.8588 (t0) REVERT: C 922 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8892 (tm-30) REVERT: C 924 ILE cc_start: 0.8408 (mm) cc_final: 0.8205 (mm) REVERT: C 926 ASN cc_start: 0.8999 (t0) cc_final: 0.8473 (t0) REVERT: C 928 GLU cc_start: 0.8807 (pp20) cc_final: 0.8574 (pp20) REVERT: C 939 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 945 GLU cc_start: 0.8315 (tt0) cc_final: 0.7217 (tt0) REVERT: C 955 VAL cc_start: 0.9081 (t) cc_final: 0.8755 (t) REVERT: C 959 PHE cc_start: 0.8704 (m-10) cc_final: 0.8356 (m-80) REVERT: C 962 ILE cc_start: 0.9003 (mm) cc_final: 0.8758 (mm) REVERT: C 964 GLU cc_start: 0.8390 (tp30) cc_final: 0.8169 (tp30) REVERT: C 965 ARG cc_start: 0.5785 (tpt170) cc_final: 0.5261 (tpm170) REVERT: C 1005 PHE cc_start: 0.8907 (t80) cc_final: 0.8210 (t80) REVERT: C 1007 ASN cc_start: 0.8838 (m110) cc_final: 0.8400 (p0) REVERT: C 1021 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6653 (ttt180) REVERT: C 1025 ASP cc_start: 0.7854 (m-30) cc_final: 0.7576 (m-30) REVERT: C 1051 ARG cc_start: 0.6965 (ttt180) cc_final: 0.5494 (ttp80) REVERT: C 1060 ARG cc_start: 0.7677 (mmt180) cc_final: 0.6587 (mpt180) REVERT: C 1063 PHE cc_start: 0.9071 (t80) cc_final: 0.8711 (t80) REVERT: C 1065 VAL cc_start: 0.9149 (t) cc_final: 0.8881 (t) REVERT: C 1088 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6877 (tm-30) outliers start: 1 outliers final: 0 residues processed: 987 average time/residue: 0.1807 time to fit residues: 268.8093 Evaluate side-chains 894 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 894 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 147 optimal weight: 0.0970 chunk 314 optimal weight: 0.7980 chunk 190 optimal weight: 0.0570 chunk 229 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 HIS ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 743 ASN ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS C 374 GLN C 395 GLN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 HIS C 638 HIS C 699 GLN C 725 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 HIS C 896 ASN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077531 restraints weight = 76631.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080564 restraints weight = 45714.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082664 restraints weight = 30415.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.084219 restraints weight = 21833.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085339 restraints weight = 16512.761| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25106 Z= 0.178 Angle : 0.662 10.273 34022 Z= 0.350 Chirality : 0.044 0.197 3789 Planarity : 0.005 0.070 4530 Dihedral : 6.582 134.520 3573 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.32 (0.15), residues: 3210 helix: 0.88 (0.12), residues: 1623 sheet: -0.33 (0.29), residues: 318 loop : -1.63 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 978 TYR 0.027 0.002 TYR B 580 PHE 0.024 0.002 PHE B 747 TRP 0.012 0.001 TRP C 382 HIS 0.014 0.002 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00373 (25106) covalent geometry : angle 0.66153 (34022) hydrogen bonds : bond 0.04423 ( 1267) hydrogen bonds : angle 4.71951 ( 3678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 975 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8434 (t70) cc_final: 0.8199 (t70) REVERT: A 56 GLU cc_start: 0.7512 (mp0) cc_final: 0.7238 (mp0) REVERT: A 63 ASN cc_start: 0.8752 (t0) cc_final: 0.8520 (t0) REVERT: A 75 GLN cc_start: 0.8986 (mt0) cc_final: 0.8491 (mp10) REVERT: A 92 GLU cc_start: 0.9075 (mp0) cc_final: 0.8810 (pm20) REVERT: A 97 MET cc_start: 0.9289 (mtt) cc_final: 0.8763 (mtt) REVERT: A 108 HIS cc_start: 0.8926 (p-80) cc_final: 0.8370 (p-80) REVERT: A 144 MET cc_start: 0.3443 (ttt) cc_final: 0.2265 (tmm) REVERT: A 182 GLN cc_start: 0.9215 (mt0) cc_final: 0.8844 (tt0) REVERT: A 232 ARG cc_start: 0.8965 (mmt90) cc_final: 0.8642 (mmt90) REVERT: A 243 ILE cc_start: 0.9133 (mt) cc_final: 0.8865 (mp) REVERT: A 254 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7101 (ttpt) REVERT: A 273 ASN cc_start: 0.8882 (m110) cc_final: 0.7998 (t0) REVERT: A 292 LEU cc_start: 0.9287 (tp) cc_final: 0.9018 (tt) REVERT: A 296 ILE cc_start: 0.9306 (mm) cc_final: 0.9094 (mm) REVERT: A 306 LEU cc_start: 0.9148 (tp) cc_final: 0.8918 (mm) REVERT: A 314 ILE cc_start: 0.8474 (pt) cc_final: 0.8241 (pt) REVERT: A 332 MET cc_start: 0.8439 (ttm) cc_final: 0.8166 (tpp) REVERT: A 346 ASP cc_start: 0.8338 (m-30) cc_final: 0.8128 (m-30) REVERT: A 357 ASN cc_start: 0.8849 (t0) cc_final: 0.8500 (t0) REVERT: A 376 GLN cc_start: 0.9221 (tt0) cc_final: 0.8366 (tp-100) REVERT: A 381 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8031 (tm-30) REVERT: A 382 TRP cc_start: 0.8178 (m-10) cc_final: 0.7884 (m-10) REVERT: A 389 MET cc_start: 0.8608 (tpt) cc_final: 0.8291 (tpt) REVERT: A 452 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8846 (mt-10) REVERT: A 470 LEU cc_start: 0.9110 (mt) cc_final: 0.8780 (mt) REVERT: A 475 GLN cc_start: 0.8727 (tp-100) cc_final: 0.7738 (tt0) REVERT: A 500 GLU cc_start: 0.9523 (tm-30) cc_final: 0.9013 (tm-30) REVERT: A 512 LEU cc_start: 0.9094 (tt) cc_final: 0.8879 (tt) REVERT: A 515 MET cc_start: 0.9092 (mmt) cc_final: 0.8268 (mmm) REVERT: A 519 MET cc_start: 0.8719 (mmt) cc_final: 0.8203 (mmp) REVERT: A 520 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7998 (mm110) REVERT: A 556 LEU cc_start: 0.9314 (mt) cc_final: 0.9079 (mt) REVERT: A 562 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 565 ILE cc_start: 0.9177 (tp) cc_final: 0.8969 (tp) REVERT: A 635 GLU cc_start: 0.8312 (mp0) cc_final: 0.8011 (mp0) REVERT: A 654 ILE cc_start: 0.8932 (pt) cc_final: 0.8642 (pt) REVERT: A 660 MET cc_start: 0.8438 (ttt) cc_final: 0.8176 (ttt) REVERT: A 667 PHE cc_start: 0.9073 (m-80) cc_final: 0.8867 (m-80) REVERT: A 690 MET cc_start: 0.9051 (mtm) cc_final: 0.8789 (mtt) REVERT: A 720 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8334 (ttm110) REVERT: A 724 LEU cc_start: 0.9494 (mm) cc_final: 0.9151 (mm) REVERT: A 725 GLN cc_start: 0.8603 (mt0) cc_final: 0.8252 (mm-40) REVERT: A 739 ASP cc_start: 0.8563 (t70) cc_final: 0.8297 (t0) REVERT: A 747 PHE cc_start: 0.8793 (m-80) cc_final: 0.8386 (m-10) REVERT: A 750 GLU cc_start: 0.9001 (pm20) cc_final: 0.8432 (pt0) REVERT: A 753 LEU cc_start: 0.9143 (mt) cc_final: 0.8905 (mt) REVERT: A 756 MET cc_start: 0.8540 (mmp) cc_final: 0.8134 (mmp) REVERT: A 761 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 794 PHE cc_start: 0.9070 (m-80) cc_final: 0.8678 (m-80) REVERT: A 798 ASN cc_start: 0.9373 (m-40) cc_final: 0.9158 (m110) REVERT: A 800 PHE cc_start: 0.9016 (m-80) cc_final: 0.8803 (m-80) REVERT: A 804 GLU cc_start: 0.7921 (pt0) cc_final: 0.7569 (pt0) REVERT: A 824 PHE cc_start: 0.9156 (p90) cc_final: 0.8531 (p90) REVERT: A 837 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8110 (mtp85) REVERT: A 841 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8135 (ttt180) REVERT: A 842 ILE cc_start: 0.9086 (mt) cc_final: 0.8694 (tp) REVERT: A 843 TRP cc_start: 0.8703 (t-100) cc_final: 0.8293 (t-100) REVERT: A 847 MET cc_start: 0.8391 (mmm) cc_final: 0.8011 (mmt) REVERT: A 882 ARG cc_start: 0.8469 (ptm-80) cc_final: 0.7849 (ptt180) REVERT: A 896 ASN cc_start: 0.8989 (m110) cc_final: 0.8734 (m110) REVERT: A 925 ILE cc_start: 0.8701 (mm) cc_final: 0.8362 (tt) REVERT: A 939 GLN cc_start: 0.8638 (tt0) cc_final: 0.8338 (tt0) REVERT: A 943 LEU cc_start: 0.8429 (pt) cc_final: 0.8102 (pt) REVERT: A 959 PHE cc_start: 0.9220 (m-80) cc_final: 0.9016 (m-80) REVERT: A 962 ILE cc_start: 0.9072 (mm) cc_final: 0.8726 (mm) REVERT: A 976 TYR cc_start: 0.8004 (t80) cc_final: 0.7682 (t80) REVERT: A 1058 ASP cc_start: 0.7610 (m-30) cc_final: 0.7291 (m-30) REVERT: A 1066 LEU cc_start: 0.9588 (mm) cc_final: 0.9368 (mm) REVERT: A 1068 ASP cc_start: 0.9228 (m-30) cc_final: 0.8701 (p0) REVERT: A 1084 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 75 GLN cc_start: 0.8986 (tt0) cc_final: 0.8573 (tt0) REVERT: B 77 ASP cc_start: 0.8327 (t70) cc_final: 0.8037 (t70) REVERT: B 127 LEU cc_start: 0.8902 (mt) cc_final: 0.8632 (mt) REVERT: B 136 TYR cc_start: 0.5892 (m-10) cc_final: 0.4777 (m-10) REVERT: B 152 ASP cc_start: 0.8746 (m-30) cc_final: 0.8517 (m-30) REVERT: B 189 ASN cc_start: 0.7533 (t0) cc_final: 0.7183 (p0) REVERT: B 200 LEU cc_start: 0.9104 (mm) cc_final: 0.8820 (tp) REVERT: B 227 ASP cc_start: 0.8430 (t70) cc_final: 0.8182 (t70) REVERT: B 228 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 266 MET cc_start: 0.8650 (pmm) cc_final: 0.8294 (pmm) REVERT: B 275 PHE cc_start: 0.8254 (t80) cc_final: 0.8011 (t80) REVERT: B 300 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8743 (mtpt) REVERT: B 314 ILE cc_start: 0.9309 (pt) cc_final: 0.9105 (pt) REVERT: B 329 LEU cc_start: 0.9001 (tp) cc_final: 0.8707 (tp) REVERT: B 331 VAL cc_start: 0.9044 (m) cc_final: 0.8720 (p) REVERT: B 345 ILE cc_start: 0.8820 (mt) cc_final: 0.8342 (mt) REVERT: B 348 LEU cc_start: 0.9456 (mt) cc_final: 0.9229 (mt) REVERT: B 349 ASP cc_start: 0.7744 (t0) cc_final: 0.7477 (t0) REVERT: B 356 ILE cc_start: 0.8825 (mp) cc_final: 0.8270 (tt) REVERT: B 362 LYS cc_start: 0.8864 (mptt) cc_final: 0.8534 (mptt) REVERT: B 365 GLN cc_start: 0.9145 (mp10) cc_final: 0.8856 (mp10) REVERT: B 389 MET cc_start: 0.8243 (mmp) cc_final: 0.7594 (mmm) REVERT: B 401 ASP cc_start: 0.8062 (t0) cc_final: 0.7810 (t0) REVERT: B 406 MET cc_start: 0.8643 (mtm) cc_final: 0.8378 (mmp) REVERT: B 448 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7985 (mtt90) REVERT: B 449 TYR cc_start: 0.9140 (p90) cc_final: 0.8883 (p90) REVERT: B 460 TYR cc_start: 0.8231 (t80) cc_final: 0.7614 (t80) REVERT: B 501 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.6960 (mmt-90) REVERT: B 504 SER cc_start: 0.7499 (t) cc_final: 0.7209 (m) REVERT: B 528 TYR cc_start: 0.7678 (t80) cc_final: 0.7112 (t80) REVERT: B 611 PHE cc_start: 0.7238 (m-10) cc_final: 0.6675 (m-10) REVERT: B 618 MET cc_start: 0.8087 (ttt) cc_final: 0.7606 (ttp) REVERT: B 621 LYS cc_start: 0.7703 (mmpt) cc_final: 0.7191 (mmpt) REVERT: B 660 MET cc_start: 0.8642 (ttt) cc_final: 0.8419 (ttt) REVERT: B 663 LEU cc_start: 0.9471 (mt) cc_final: 0.9221 (mt) REVERT: B 667 PHE cc_start: 0.7932 (m-80) cc_final: 0.7124 (m-80) REVERT: B 687 ILE cc_start: 0.8848 (mm) cc_final: 0.8300 (mm) REVERT: B 688 LEU cc_start: 0.9231 (tp) cc_final: 0.8733 (tp) REVERT: B 690 MET cc_start: 0.7698 (mtm) cc_final: 0.7347 (mtm) REVERT: B 697 ASP cc_start: 0.8815 (m-30) cc_final: 0.8579 (m-30) REVERT: B 704 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7940 (ttt180) REVERT: B 716 GLU cc_start: 0.8758 (tt0) cc_final: 0.8268 (tm-30) REVERT: B 753 LEU cc_start: 0.9013 (mt) cc_final: 0.8788 (mt) REVERT: B 755 VAL cc_start: 0.9528 (t) cc_final: 0.9266 (t) REVERT: B 779 TYR cc_start: 0.7887 (t80) cc_final: 0.7121 (t80) REVERT: B 796 LEU cc_start: 0.9229 (mt) cc_final: 0.8644 (mt) REVERT: B 800 PHE cc_start: 0.8720 (m-80) cc_final: 0.8294 (m-80) REVERT: B 814 ASP cc_start: 0.8936 (m-30) cc_final: 0.8608 (p0) REVERT: B 822 PHE cc_start: 0.7963 (m-80) cc_final: 0.7715 (m-80) REVERT: B 826 ASN cc_start: 0.8752 (p0) cc_final: 0.8463 (p0) REVERT: B 828 MET cc_start: 0.7792 (tmm) cc_final: 0.7185 (tpt) REVERT: B 829 ASP cc_start: 0.8090 (t0) cc_final: 0.7568 (t0) REVERT: B 831 GLU cc_start: 0.8845 (mp0) cc_final: 0.8472 (mp0) REVERT: B 841 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7618 (ptm160) REVERT: B 848 ARG cc_start: 0.8861 (tmt170) cc_final: 0.8277 (tpp80) REVERT: B 859 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8195 (mtmt) REVERT: B 889 ILE cc_start: 0.9045 (pt) cc_final: 0.8811 (pt) REVERT: B 894 ASN cc_start: 0.8137 (m-40) cc_final: 0.7918 (m-40) REVERT: B 946 GLU cc_start: 0.8688 (tp30) cc_final: 0.7818 (tp30) REVERT: B 958 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9098 (tp30) REVERT: B 981 ILE cc_start: 0.9560 (mm) cc_final: 0.9238 (tp) REVERT: B 984 GLU cc_start: 0.9092 (pt0) cc_final: 0.8567 (pp20) REVERT: B 1027 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8975 (mttt) REVERT: B 1036 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 1054 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 1058 ASP cc_start: 0.8779 (m-30) cc_final: 0.8257 (m-30) REVERT: B 1066 LEU cc_start: 0.9311 (mm) cc_final: 0.9063 (mm) REVERT: B 1067 MET cc_start: 0.8823 (mmp) cc_final: 0.8269 (mmp) REVERT: C 29 PHE cc_start: 0.8617 (m-80) cc_final: 0.8058 (m-10) REVERT: C 66 VAL cc_start: 0.9045 (t) cc_final: 0.8054 (m) REVERT: C 112 PHE cc_start: 0.8306 (m-80) cc_final: 0.7932 (m-80) REVERT: C 161 LEU cc_start: 0.8644 (mp) cc_final: 0.8123 (tp) REVERT: C 230 ILE cc_start: 0.8864 (mm) cc_final: 0.8370 (tt) REVERT: C 292 LEU cc_start: 0.7260 (mt) cc_final: 0.7043 (mp) REVERT: C 326 ASP cc_start: 0.5066 (t0) cc_final: 0.4677 (p0) REVERT: C 347 MET cc_start: 0.6604 (mmt) cc_final: 0.6114 (mmt) REVERT: C 376 GLN cc_start: 0.7887 (tt0) cc_final: 0.7549 (tm-30) REVERT: C 389 MET cc_start: 0.8521 (tpt) cc_final: 0.8206 (tpt) REVERT: C 401 ASP cc_start: 0.7974 (t0) cc_final: 0.7709 (t0) REVERT: C 406 MET cc_start: 0.7718 (tpp) cc_final: 0.7509 (tpp) REVERT: C 420 MET cc_start: 0.6291 (mpp) cc_final: 0.5777 (mpp) REVERT: C 460 TYR cc_start: 0.7938 (t80) cc_final: 0.7455 (t80) REVERT: C 477 LEU cc_start: 0.9449 (mt) cc_final: 0.9123 (mt) REVERT: C 497 LEU cc_start: 0.8646 (mt) cc_final: 0.8108 (mm) REVERT: C 500 GLU cc_start: 0.9445 (tt0) cc_final: 0.9170 (mt-10) REVERT: C 515 MET cc_start: 0.8925 (mmp) cc_final: 0.8722 (mmp) REVERT: C 520 GLN cc_start: 0.8961 (mm110) cc_final: 0.7972 (mm110) REVERT: C 524 SER cc_start: 0.9365 (m) cc_final: 0.9113 (p) REVERT: C 555 VAL cc_start: 0.9107 (t) cc_final: 0.8879 (t) REVERT: C 569 LEU cc_start: 0.8482 (pp) cc_final: 0.8278 (pp) REVERT: C 570 MET cc_start: 0.9075 (tpp) cc_final: 0.8367 (tpp) REVERT: C 572 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8032 (mt-10) REVERT: C 633 TYR cc_start: 0.8171 (m-80) cc_final: 0.7791 (m-80) REVERT: C 678 MET cc_start: 0.6892 (pmm) cc_final: 0.6588 (pmm) REVERT: C 749 THR cc_start: 0.9089 (p) cc_final: 0.8849 (p) REVERT: C 750 GLU cc_start: 0.8757 (pm20) cc_final: 0.8032 (mp0) REVERT: C 756 MET cc_start: 0.9047 (mmm) cc_final: 0.8425 (tmm) REVERT: C 763 PHE cc_start: 0.8674 (m-10) cc_final: 0.8332 (m-80) REVERT: C 794 PHE cc_start: 0.9050 (m-10) cc_final: 0.8431 (m-10) REVERT: C 806 TYR cc_start: 0.8043 (m-10) cc_final: 0.7194 (m-80) REVERT: C 826 ASN cc_start: 0.7787 (m110) cc_final: 0.7452 (m110) REVERT: C 835 LEU cc_start: 0.8647 (tp) cc_final: 0.8389 (tp) REVERT: C 841 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8319 (ttm170) REVERT: C 859 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8548 (mtpt) REVERT: C 875 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6659 (mt-10) REVERT: C 878 PHE cc_start: 0.8766 (m-80) cc_final: 0.6994 (m-80) REVERT: C 894 ASN cc_start: 0.8794 (m-40) cc_final: 0.8583 (t0) REVERT: C 921 ILE cc_start: 0.9083 (tp) cc_final: 0.8805 (tp) REVERT: C 922 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 924 ILE cc_start: 0.8505 (mm) cc_final: 0.8221 (mm) REVERT: C 925 ILE cc_start: 0.9277 (mp) cc_final: 0.9075 (mp) REVERT: C 926 ASN cc_start: 0.8971 (t0) cc_final: 0.8466 (t0) REVERT: C 928 GLU cc_start: 0.8885 (pp20) cc_final: 0.7846 (pp20) REVERT: C 939 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7819 (tm-30) REVERT: C 945 GLU cc_start: 0.8214 (tt0) cc_final: 0.7481 (tt0) REVERT: C 949 ASP cc_start: 0.9073 (m-30) cc_final: 0.8828 (m-30) REVERT: C 955 VAL cc_start: 0.9058 (t) cc_final: 0.8789 (t) REVERT: C 959 PHE cc_start: 0.8749 (m-10) cc_final: 0.8411 (m-80) REVERT: C 962 ILE cc_start: 0.9044 (mm) cc_final: 0.8825 (mm) REVERT: C 964 GLU cc_start: 0.8426 (tp30) cc_final: 0.8167 (tp30) REVERT: C 965 ARG cc_start: 0.5954 (tpt170) cc_final: 0.5169 (tpm170) REVERT: C 1005 PHE cc_start: 0.8932 (t80) cc_final: 0.8256 (t80) REVERT: C 1007 ASN cc_start: 0.8904 (m110) cc_final: 0.8430 (p0) REVERT: C 1021 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6563 (ttt-90) REVERT: C 1025 ASP cc_start: 0.8082 (m-30) cc_final: 0.7769 (m-30) REVERT: C 1051 ARG cc_start: 0.6982 (ttt180) cc_final: 0.6621 (ttt180) REVERT: C 1060 ARG cc_start: 0.7396 (mmt180) cc_final: 0.6476 (mmt180) REVERT: C 1063 PHE cc_start: 0.9154 (t80) cc_final: 0.8829 (t80) outliers start: 2 outliers final: 1 residues processed: 975 average time/residue: 0.1989 time to fit residues: 290.3385 Evaluate side-chains 885 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 884 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 293 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 0.0470 chunk 74 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 HIS A1059 ASN A1088 GLN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN C 374 GLN ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 HIS C 886 GLN C 896 ASN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079495 restraints weight = 76056.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082559 restraints weight = 45335.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084739 restraints weight = 30179.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086320 restraints weight = 21576.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087480 restraints weight = 16276.384| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25106 Z= 0.140 Angle : 0.651 9.489 34022 Z= 0.339 Chirality : 0.043 0.187 3789 Planarity : 0.005 0.054 4530 Dihedral : 6.438 133.914 3573 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.23 (0.15), residues: 3210 helix: 0.97 (0.13), residues: 1623 sheet: -0.45 (0.31), residues: 285 loop : -1.54 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 433 TYR 0.029 0.002 TYR A 93 PHE 0.040 0.002 PHE A 233 TRP 0.017 0.001 TRP B 843 HIS 0.008 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00299 (25106) covalent geometry : angle 0.65076 (34022) hydrogen bonds : bond 0.04226 ( 1267) hydrogen bonds : angle 4.56557 ( 3678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 950 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8290 (m-80) cc_final: 0.7973 (m-80) REVERT: A 56 GLU cc_start: 0.7490 (mp0) cc_final: 0.7066 (mp0) REVERT: A 75 GLN cc_start: 0.8999 (mt0) cc_final: 0.8486 (mp10) REVERT: A 92 GLU cc_start: 0.9063 (mp0) cc_final: 0.8637 (pm20) REVERT: A 97 MET cc_start: 0.9317 (mtt) cc_final: 0.8868 (mtm) REVERT: A 108 HIS cc_start: 0.8884 (p-80) cc_final: 0.8267 (p-80) REVERT: A 144 MET cc_start: 0.3582 (ttt) cc_final: 0.2750 (tmm) REVERT: A 178 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8537 (mtm180) REVERT: A 182 GLN cc_start: 0.9257 (mt0) cc_final: 0.8447 (tp40) REVERT: A 222 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7931 (ptpp) REVERT: A 232 ARG cc_start: 0.9062 (mmt90) cc_final: 0.8714 (mmt90) REVERT: A 241 LEU cc_start: 0.9036 (mt) cc_final: 0.8745 (mm) REVERT: A 243 ILE cc_start: 0.9088 (mt) cc_final: 0.8821 (mp) REVERT: A 254 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8149 (ttpt) REVERT: A 264 ILE cc_start: 0.9117 (tp) cc_final: 0.8703 (tp) REVERT: A 273 ASN cc_start: 0.8886 (m110) cc_final: 0.8019 (t0) REVERT: A 292 LEU cc_start: 0.9270 (tp) cc_final: 0.9057 (tt) REVERT: A 306 LEU cc_start: 0.9250 (tp) cc_final: 0.8811 (mm) REVERT: A 368 TRP cc_start: 0.8934 (t60) cc_final: 0.8603 (t60) REVERT: A 376 GLN cc_start: 0.9129 (tt0) cc_final: 0.8241 (tp-100) REVERT: A 381 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8006 (tm-30) REVERT: A 382 TRP cc_start: 0.8175 (m-10) cc_final: 0.7875 (m-10) REVERT: A 389 MET cc_start: 0.8581 (tpt) cc_final: 0.8170 (tpt) REVERT: A 401 ASP cc_start: 0.8287 (t0) cc_final: 0.8040 (t0) REVERT: A 470 LEU cc_start: 0.9096 (mt) cc_final: 0.8767 (mt) REVERT: A 475 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8041 (tt0) REVERT: A 482 ASP cc_start: 0.9009 (m-30) cc_final: 0.8757 (m-30) REVERT: A 500 GLU cc_start: 0.9517 (tm-30) cc_final: 0.8993 (tm-30) REVERT: A 512 LEU cc_start: 0.9083 (tt) cc_final: 0.8881 (tt) REVERT: A 515 MET cc_start: 0.9028 (mmt) cc_final: 0.8711 (mmm) REVERT: A 518 GLN cc_start: 0.9121 (mp10) cc_final: 0.8904 (mp10) REVERT: A 519 MET cc_start: 0.8751 (mmt) cc_final: 0.8417 (mmm) REVERT: A 555 VAL cc_start: 0.9189 (t) cc_final: 0.8985 (t) REVERT: A 565 ILE cc_start: 0.9079 (tp) cc_final: 0.8723 (tp) REVERT: A 611 PHE cc_start: 0.8368 (m-80) cc_final: 0.7852 (m-80) REVERT: A 635 GLU cc_start: 0.8340 (mp0) cc_final: 0.8066 (mp0) REVERT: A 654 ILE cc_start: 0.8900 (pt) cc_final: 0.8614 (pt) REVERT: A 660 MET cc_start: 0.8453 (ttt) cc_final: 0.7962 (ttt) REVERT: A 690 MET cc_start: 0.9012 (mtm) cc_final: 0.8448 (mtm) REVERT: A 700 ILE cc_start: 0.8894 (mm) cc_final: 0.8676 (pt) REVERT: A 720 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8280 (ttm110) REVERT: A 724 LEU cc_start: 0.9506 (mm) cc_final: 0.9076 (mm) REVERT: A 725 GLN cc_start: 0.8585 (mt0) cc_final: 0.8228 (mm-40) REVERT: A 735 ILE cc_start: 0.9298 (mm) cc_final: 0.9089 (mm) REVERT: A 747 PHE cc_start: 0.8771 (m-80) cc_final: 0.8370 (m-10) REVERT: A 750 GLU cc_start: 0.8974 (pm20) cc_final: 0.8435 (pt0) REVERT: A 753 LEU cc_start: 0.9139 (mt) cc_final: 0.8907 (mt) REVERT: A 756 MET cc_start: 0.8503 (mmp) cc_final: 0.8090 (mmp) REVERT: A 761 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 794 PHE cc_start: 0.9018 (m-80) cc_final: 0.8655 (m-80) REVERT: A 798 ASN cc_start: 0.9377 (m-40) cc_final: 0.9109 (m110) REVERT: A 804 GLU cc_start: 0.7922 (pt0) cc_final: 0.7624 (pt0) REVERT: A 837 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7926 (mmm-85) REVERT: A 841 ARG cc_start: 0.9077 (ttm170) cc_final: 0.8331 (ttt180) REVERT: A 842 ILE cc_start: 0.9064 (mt) cc_final: 0.8663 (tp) REVERT: A 843 TRP cc_start: 0.8662 (t-100) cc_final: 0.8244 (t-100) REVERT: A 847 MET cc_start: 0.8287 (mmm) cc_final: 0.7952 (mmt) REVERT: A 854 ASN cc_start: 0.8252 (t0) cc_final: 0.7884 (t0) REVERT: A 882 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.7771 (ptt180) REVERT: A 894 ASN cc_start: 0.9007 (t0) cc_final: 0.8421 (t0) REVERT: A 896 ASN cc_start: 0.9043 (m110) cc_final: 0.8767 (m110) REVERT: A 916 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8414 (ttm-80) REVERT: A 925 ILE cc_start: 0.8708 (mm) cc_final: 0.8323 (tt) REVERT: A 939 GLN cc_start: 0.8615 (tt0) cc_final: 0.8314 (tt0) REVERT: A 946 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 962 ILE cc_start: 0.9035 (mm) cc_final: 0.8776 (mm) REVERT: A 976 TYR cc_start: 0.7808 (t80) cc_final: 0.7522 (t80) REVERT: A 1058 ASP cc_start: 0.7351 (m-30) cc_final: 0.7081 (m-30) REVERT: A 1066 LEU cc_start: 0.9540 (mm) cc_final: 0.9338 (mm) REVERT: A 1068 ASP cc_start: 0.9225 (m-30) cc_final: 0.8739 (p0) REVERT: A 1084 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 1088 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (pp30) REVERT: B 75 GLN cc_start: 0.8988 (tt0) cc_final: 0.8620 (tt0) REVERT: B 77 ASP cc_start: 0.8354 (t70) cc_final: 0.8062 (t70) REVERT: B 102 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8454 (ttp80) REVERT: B 127 LEU cc_start: 0.8966 (mt) cc_final: 0.8665 (mt) REVERT: B 149 MET cc_start: 0.7677 (ppp) cc_final: 0.6924 (ppp) REVERT: B 155 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8896 (mm-40) REVERT: B 178 ARG cc_start: 0.9132 (tpt-90) cc_final: 0.8836 (tpt-90) REVERT: B 189 ASN cc_start: 0.7422 (t0) cc_final: 0.7160 (p0) REVERT: B 200 LEU cc_start: 0.9079 (mm) cc_final: 0.8803 (tp) REVERT: B 228 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8462 (mm-30) REVERT: B 274 ILE cc_start: 0.8544 (mp) cc_final: 0.8342 (mm) REVERT: B 300 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8701 (mtpt) REVERT: B 314 ILE cc_start: 0.9339 (pt) cc_final: 0.9093 (pt) REVERT: B 328 SER cc_start: 0.9154 (m) cc_final: 0.8947 (p) REVERT: B 329 LEU cc_start: 0.8931 (tp) cc_final: 0.8665 (tp) REVERT: B 336 PHE cc_start: 0.8042 (p90) cc_final: 0.7561 (p90) REVERT: B 342 LEU cc_start: 0.9234 (pt) cc_final: 0.9020 (pt) REVERT: B 345 ILE cc_start: 0.8778 (mt) cc_final: 0.8268 (mt) REVERT: B 348 LEU cc_start: 0.9421 (mt) cc_final: 0.9221 (mt) REVERT: B 349 ASP cc_start: 0.7846 (t0) cc_final: 0.7624 (t0) REVERT: B 356 ILE cc_start: 0.8788 (mp) cc_final: 0.8105 (tt) REVERT: B 365 GLN cc_start: 0.9132 (mp10) cc_final: 0.8847 (mp10) REVERT: B 374 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8923 (tp-100) REVERT: B 377 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7848 (ttm170) REVERT: B 389 MET cc_start: 0.8156 (mmp) cc_final: 0.7525 (mmm) REVERT: B 401 ASP cc_start: 0.8121 (t0) cc_final: 0.7831 (t0) REVERT: B 406 MET cc_start: 0.8655 (mtm) cc_final: 0.8379 (mmp) REVERT: B 460 TYR cc_start: 0.8200 (t80) cc_final: 0.7594 (t80) REVERT: B 501 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7038 (mmt-90) REVERT: B 504 SER cc_start: 0.7455 (t) cc_final: 0.7240 (m) REVERT: B 510 ARG cc_start: 0.8913 (mtp180) cc_final: 0.8148 (mtp85) REVERT: B 512 LEU cc_start: 0.9539 (mm) cc_final: 0.9199 (pp) REVERT: B 528 TYR cc_start: 0.7604 (t80) cc_final: 0.7079 (t80) REVERT: B 611 PHE cc_start: 0.7209 (m-10) cc_final: 0.6615 (m-10) REVERT: B 618 MET cc_start: 0.8452 (ttm) cc_final: 0.7965 (ttt) REVERT: B 621 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7135 (mmpt) REVERT: B 660 MET cc_start: 0.8656 (ttt) cc_final: 0.8329 (ttm) REVERT: B 663 LEU cc_start: 0.9466 (mt) cc_final: 0.9216 (mt) REVERT: B 667 PHE cc_start: 0.7705 (m-80) cc_final: 0.7116 (m-80) REVERT: B 687 ILE cc_start: 0.8826 (mm) cc_final: 0.8308 (mm) REVERT: B 688 LEU cc_start: 0.9247 (tp) cc_final: 0.8582 (tp) REVERT: B 690 MET cc_start: 0.7628 (mtm) cc_final: 0.7317 (mtm) REVERT: B 692 MET cc_start: 0.8691 (mmp) cc_final: 0.8473 (mmp) REVERT: B 697 ASP cc_start: 0.8947 (m-30) cc_final: 0.8649 (m-30) REVERT: B 716 GLU cc_start: 0.8726 (tt0) cc_final: 0.8204 (tm-30) REVERT: B 753 LEU cc_start: 0.8955 (mt) cc_final: 0.8665 (mt) REVERT: B 755 VAL cc_start: 0.9532 (t) cc_final: 0.9292 (t) REVERT: B 779 TYR cc_start: 0.7813 (t80) cc_final: 0.7035 (t80) REVERT: B 796 LEU cc_start: 0.9215 (mt) cc_final: 0.8776 (mt) REVERT: B 814 ASP cc_start: 0.8922 (m-30) cc_final: 0.8602 (p0) REVERT: B 822 PHE cc_start: 0.7931 (m-80) cc_final: 0.7729 (m-80) REVERT: B 826 ASN cc_start: 0.8703 (p0) cc_final: 0.8416 (p0) REVERT: B 828 MET cc_start: 0.7776 (tmm) cc_final: 0.7208 (tpt) REVERT: B 829 ASP cc_start: 0.8101 (t0) cc_final: 0.7707 (t0) REVERT: B 837 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8803 (mtp85) REVERT: B 841 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7509 (ptm160) REVERT: B 848 ARG cc_start: 0.8820 (tmt170) cc_final: 0.8289 (tpp80) REVERT: B 854 ASN cc_start: 0.9000 (t0) cc_final: 0.8785 (t0) REVERT: B 858 GLN cc_start: 0.8716 (pp30) cc_final: 0.8453 (tm-30) REVERT: B 859 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8353 (mtmt) REVERT: B 945 GLU cc_start: 0.7933 (pm20) cc_final: 0.7682 (mp0) REVERT: B 946 GLU cc_start: 0.8614 (tp30) cc_final: 0.7844 (tp30) REVERT: B 958 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9254 (tp30) REVERT: B 981 ILE cc_start: 0.9565 (mm) cc_final: 0.9239 (tp) REVERT: B 984 GLU cc_start: 0.9116 (pt0) cc_final: 0.8553 (pp20) REVERT: B 1036 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8663 (mt-10) REVERT: B 1054 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8458 (tm-30) REVERT: B 1058 ASP cc_start: 0.8729 (m-30) cc_final: 0.8117 (m-30) REVERT: B 1067 MET cc_start: 0.8689 (mmp) cc_final: 0.8342 (mmp) REVERT: C 29 PHE cc_start: 0.8575 (m-80) cc_final: 0.8048 (m-10) REVERT: C 66 VAL cc_start: 0.8959 (t) cc_final: 0.8003 (m) REVERT: C 112 PHE cc_start: 0.8349 (m-80) cc_final: 0.8078 (m-80) REVERT: C 161 LEU cc_start: 0.8651 (mp) cc_final: 0.8157 (tp) REVERT: C 227 ASP cc_start: 0.8235 (t0) cc_final: 0.7771 (t0) REVERT: C 230 ILE cc_start: 0.8816 (mm) cc_final: 0.8157 (tt) REVERT: C 326 ASP cc_start: 0.5335 (t0) cc_final: 0.4877 (p0) REVERT: C 389 MET cc_start: 0.8464 (tpt) cc_final: 0.8153 (tpt) REVERT: C 460 TYR cc_start: 0.7952 (t80) cc_final: 0.7428 (t80) REVERT: C 477 LEU cc_start: 0.9413 (mt) cc_final: 0.9138 (mt) REVERT: C 520 GLN cc_start: 0.8897 (mm110) cc_final: 0.7907 (mm110) REVERT: C 524 SER cc_start: 0.9368 (m) cc_final: 0.9053 (p) REVERT: C 555 VAL cc_start: 0.9148 (t) cc_final: 0.8937 (t) REVERT: C 569 LEU cc_start: 0.8511 (pp) cc_final: 0.8294 (pp) REVERT: C 570 MET cc_start: 0.9062 (tpp) cc_final: 0.8336 (tpp) REVERT: C 572 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 633 TYR cc_start: 0.8066 (m-80) cc_final: 0.7612 (m-80) REVERT: C 678 MET cc_start: 0.6837 (pmm) cc_final: 0.6428 (pmm) REVERT: C 724 LEU cc_start: 0.9107 (mp) cc_final: 0.8878 (tp) REVERT: C 750 GLU cc_start: 0.8867 (pm20) cc_final: 0.8611 (mp0) REVERT: C 756 MET cc_start: 0.9036 (mmm) cc_final: 0.8397 (tmm) REVERT: C 763 PHE cc_start: 0.8619 (m-10) cc_final: 0.8272 (m-80) REVERT: C 791 GLN cc_start: 0.8876 (tt0) cc_final: 0.8561 (tt0) REVERT: C 794 PHE cc_start: 0.9040 (m-10) cc_final: 0.8532 (m-10) REVERT: C 806 TYR cc_start: 0.8028 (m-10) cc_final: 0.7189 (m-80) REVERT: C 826 ASN cc_start: 0.7682 (m110) cc_final: 0.7480 (m110) REVERT: C 835 LEU cc_start: 0.8510 (tp) cc_final: 0.8247 (tp) REVERT: C 841 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8362 (ttm170) REVERT: C 875 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6663 (mt-10) REVERT: C 878 PHE cc_start: 0.8786 (m-80) cc_final: 0.7129 (m-80) REVERT: C 922 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8916 (tm-30) REVERT: C 925 ILE cc_start: 0.9237 (mp) cc_final: 0.9010 (mp) REVERT: C 926 ASN cc_start: 0.8876 (t0) cc_final: 0.8340 (t0) REVERT: C 939 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 945 GLU cc_start: 0.8291 (tt0) cc_final: 0.7502 (tt0) REVERT: C 949 ASP cc_start: 0.9034 (m-30) cc_final: 0.8810 (m-30) REVERT: C 955 VAL cc_start: 0.9179 (t) cc_final: 0.8890 (t) REVERT: C 959 PHE cc_start: 0.8682 (m-10) cc_final: 0.8385 (m-80) REVERT: C 962 ILE cc_start: 0.9030 (mm) cc_final: 0.8794 (mm) REVERT: C 964 GLU cc_start: 0.8345 (tp30) cc_final: 0.8067 (tp30) REVERT: C 965 ARG cc_start: 0.5720 (tpt170) cc_final: 0.5001 (tpm170) REVERT: C 977 GLN cc_start: 0.8901 (mp10) cc_final: 0.8414 (mp10) REVERT: C 989 GLU cc_start: 0.8459 (tp30) cc_final: 0.8202 (tp30) REVERT: C 1005 PHE cc_start: 0.8921 (t80) cc_final: 0.8101 (t80) REVERT: C 1007 ASN cc_start: 0.8936 (m110) cc_final: 0.8568 (p0) REVERT: C 1021 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6751 (ttt90) REVERT: C 1025 ASP cc_start: 0.8266 (m-30) cc_final: 0.7989 (m-30) REVERT: C 1030 GLN cc_start: 0.8939 (mp10) cc_final: 0.8657 (mp10) REVERT: C 1051 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6488 (ttt180) REVERT: C 1060 ARG cc_start: 0.7362 (mmt180) cc_final: 0.6653 (mmt180) REVERT: C 1063 PHE cc_start: 0.9139 (t80) cc_final: 0.8855 (t80) outliers start: 2 outliers final: 0 residues processed: 952 average time/residue: 0.2002 time to fit residues: 284.5178 Evaluate side-chains 871 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 870 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 HIS ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 HIS B 743 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 872 HIS C 886 GLN C 896 ASN ** C 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076885 restraints weight = 79295.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079837 restraints weight = 47584.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081944 restraints weight = 31809.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083446 restraints weight = 22828.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084548 restraints weight = 17322.650| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25106 Z= 0.242 Angle : 0.719 9.319 34022 Z= 0.384 Chirality : 0.045 0.185 3789 Planarity : 0.005 0.064 4530 Dihedral : 6.672 131.474 3573 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.64 (0.14), residues: 3210 helix: 0.61 (0.12), residues: 1629 sheet: -0.59 (0.31), residues: 285 loop : -1.73 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 377 TYR 0.034 0.002 TYR C 93 PHE 0.056 0.002 PHE A 611 TRP 0.017 0.002 TRP C 382 HIS 0.009 0.002 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00494 (25106) covalent geometry : angle 0.71869 (34022) hydrogen bonds : bond 0.04590 ( 1267) hydrogen bonds : angle 5.01464 ( 3678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 930 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7643 (mp0) cc_final: 0.7255 (mp0) REVERT: A 60 LEU cc_start: 0.8210 (pp) cc_final: 0.8007 (pp) REVERT: A 64 ARG cc_start: 0.7788 (mmt90) cc_final: 0.7281 (mmt90) REVERT: A 75 GLN cc_start: 0.9003 (mt0) cc_final: 0.8509 (mp10) REVERT: A 92 GLU cc_start: 0.9037 (mp0) cc_final: 0.8750 (pm20) REVERT: A 97 MET cc_start: 0.9260 (mtt) cc_final: 0.8683 (mtp) REVERT: A 108 HIS cc_start: 0.8922 (p-80) cc_final: 0.8409 (p-80) REVERT: A 182 GLN cc_start: 0.9254 (mt0) cc_final: 0.8471 (tp40) REVERT: A 222 LYS cc_start: 0.8566 (ptpp) cc_final: 0.8227 (ptpp) REVERT: A 232 ARG cc_start: 0.9033 (mmt90) cc_final: 0.8826 (mmt90) REVERT: A 243 ILE cc_start: 0.9131 (mt) cc_final: 0.8889 (mp) REVERT: A 249 ASP cc_start: 0.8176 (m-30) cc_final: 0.7940 (m-30) REVERT: A 254 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8049 (ttpt) REVERT: A 273 ASN cc_start: 0.8933 (m110) cc_final: 0.8157 (t0) REVERT: A 292 LEU cc_start: 0.9316 (tp) cc_final: 0.9060 (tt) REVERT: A 306 LEU cc_start: 0.9084 (tp) cc_final: 0.8883 (tp) REVERT: A 375 VAL cc_start: 0.9132 (t) cc_final: 0.8896 (t) REVERT: A 376 GLN cc_start: 0.9179 (tt0) cc_final: 0.8351 (tp-100) REVERT: A 381 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8091 (tm-30) REVERT: A 389 MET cc_start: 0.8544 (tpt) cc_final: 0.8226 (tpt) REVERT: A 401 ASP cc_start: 0.8366 (t0) cc_final: 0.8056 (t0) REVERT: A 452 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8885 (mt-10) REVERT: A 470 LEU cc_start: 0.9080 (mt) cc_final: 0.8764 (mt) REVERT: A 475 GLN cc_start: 0.8767 (tp-100) cc_final: 0.7512 (tt0) REVERT: A 500 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9014 (tm-30) REVERT: A 515 MET cc_start: 0.9103 (mmt) cc_final: 0.8579 (mmm) REVERT: A 519 MET cc_start: 0.8776 (mmt) cc_final: 0.8200 (mmm) REVERT: A 562 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 565 ILE cc_start: 0.9149 (tp) cc_final: 0.8867 (tp) REVERT: A 611 PHE cc_start: 0.8243 (m-80) cc_final: 0.7995 (m-80) REVERT: A 623 LEU cc_start: 0.9220 (tp) cc_final: 0.8921 (mm) REVERT: A 654 ILE cc_start: 0.8960 (pt) cc_final: 0.8635 (pt) REVERT: A 657 LEU cc_start: 0.8598 (tp) cc_final: 0.8392 (tp) REVERT: A 660 MET cc_start: 0.8450 (ttt) cc_final: 0.8052 (ttt) REVERT: A 667 PHE cc_start: 0.9001 (m-80) cc_final: 0.8680 (m-80) REVERT: A 690 MET cc_start: 0.9055 (mtm) cc_final: 0.8645 (mtt) REVERT: A 720 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.8462 (ttm110) REVERT: A 724 LEU cc_start: 0.9506 (mm) cc_final: 0.9169 (mm) REVERT: A 725 GLN cc_start: 0.8567 (mt0) cc_final: 0.8165 (mm-40) REVERT: A 739 ASP cc_start: 0.8637 (t70) cc_final: 0.8313 (t0) REVERT: A 747 PHE cc_start: 0.8818 (m-80) cc_final: 0.8414 (m-10) REVERT: A 750 GLU cc_start: 0.9010 (pm20) cc_final: 0.8460 (pt0) REVERT: A 756 MET cc_start: 0.8380 (mmp) cc_final: 0.8053 (mmp) REVERT: A 761 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 794 PHE cc_start: 0.8999 (m-80) cc_final: 0.8712 (m-80) REVERT: A 804 GLU cc_start: 0.7996 (pt0) cc_final: 0.7648 (pt0) REVERT: A 824 PHE cc_start: 0.9193 (p90) cc_final: 0.8476 (p90) REVERT: A 837 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8151 (mmm-85) REVERT: A 841 ARG cc_start: 0.9238 (ttm170) cc_final: 0.8494 (ttt180) REVERT: A 842 ILE cc_start: 0.9100 (mt) cc_final: 0.8630 (tp) REVERT: A 843 TRP cc_start: 0.8769 (t-100) cc_final: 0.8423 (t-100) REVERT: A 847 MET cc_start: 0.8427 (mmm) cc_final: 0.8107 (mmt) REVERT: A 882 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.7887 (ptt180) REVERT: A 894 ASN cc_start: 0.8999 (t0) cc_final: 0.8559 (t0) REVERT: A 925 ILE cc_start: 0.8747 (mm) cc_final: 0.8467 (tt) REVERT: A 939 GLN cc_start: 0.8680 (tt0) cc_final: 0.8359 (tt0) REVERT: A 946 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 959 PHE cc_start: 0.9260 (m-80) cc_final: 0.8760 (m-80) REVERT: A 962 ILE cc_start: 0.9094 (mm) cc_final: 0.8771 (mm) REVERT: A 976 TYR cc_start: 0.7973 (t80) cc_final: 0.7649 (t80) REVERT: A 980 LYS cc_start: 0.9270 (tttt) cc_final: 0.9038 (tttt) REVERT: A 1036 GLU cc_start: 0.8317 (tp30) cc_final: 0.7942 (tp30) REVERT: A 1058 ASP cc_start: 0.7791 (m-30) cc_final: 0.7489 (m-30) REVERT: A 1068 ASP cc_start: 0.9207 (m-30) cc_final: 0.8804 (p0) REVERT: A 1084 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8515 (mm-30) REVERT: A 1092 ASN cc_start: 0.8358 (p0) cc_final: 0.8080 (p0) REVERT: B 75 GLN cc_start: 0.9073 (tt0) cc_final: 0.8578 (tt0) REVERT: B 77 ASP cc_start: 0.8243 (t70) cc_final: 0.7867 (t70) REVERT: B 127 LEU cc_start: 0.8928 (mt) cc_final: 0.8591 (mt) REVERT: B 155 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8947 (mm-40) REVERT: B 200 LEU cc_start: 0.9154 (mm) cc_final: 0.8881 (tp) REVERT: B 228 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8490 (mm-30) REVERT: B 266 MET cc_start: 0.8387 (pmm) cc_final: 0.8033 (pmm) REVERT: B 300 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8793 (mtpt) REVERT: B 336 PHE cc_start: 0.8120 (p90) cc_final: 0.7585 (p90) REVERT: B 345 ILE cc_start: 0.8874 (mt) cc_final: 0.8345 (mt) REVERT: B 348 LEU cc_start: 0.9497 (mt) cc_final: 0.9195 (mt) REVERT: B 349 ASP cc_start: 0.7737 (t0) cc_final: 0.7429 (t0) REVERT: B 356 ILE cc_start: 0.8824 (mp) cc_final: 0.8203 (tt) REVERT: B 365 GLN cc_start: 0.9202 (mp10) cc_final: 0.8833 (mp10) REVERT: B 374 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8903 (tp-100) REVERT: B 389 MET cc_start: 0.8203 (mmp) cc_final: 0.7645 (mmm) REVERT: B 448 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7934 (mtt90) REVERT: B 504 SER cc_start: 0.7850 (t) cc_final: 0.7621 (m) REVERT: B 510 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8182 (mtp85) REVERT: B 528 TYR cc_start: 0.7680 (t80) cc_final: 0.7183 (t80) REVERT: B 611 PHE cc_start: 0.7195 (m-10) cc_final: 0.6718 (m-10) REVERT: B 618 MET cc_start: 0.8396 (ttm) cc_final: 0.7809 (ttt) REVERT: B 621 LYS cc_start: 0.7830 (mmpt) cc_final: 0.6772 (mmpt) REVERT: B 660 MET cc_start: 0.8681 (ttt) cc_final: 0.8395 (ttm) REVERT: B 663 LEU cc_start: 0.9473 (mt) cc_final: 0.9236 (mt) REVERT: B 667 PHE cc_start: 0.7648 (m-80) cc_final: 0.7076 (m-80) REVERT: B 687 ILE cc_start: 0.8647 (mm) cc_final: 0.8079 (mm) REVERT: B 688 LEU cc_start: 0.9197 (tp) cc_final: 0.8983 (pp) REVERT: B 690 MET cc_start: 0.7675 (mtm) cc_final: 0.7351 (mtm) REVERT: B 697 ASP cc_start: 0.8968 (m-30) cc_final: 0.8663 (m-30) REVERT: B 704 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7976 (ttt180) REVERT: B 716 GLU cc_start: 0.8752 (tt0) cc_final: 0.8276 (tm-30) REVERT: B 731 VAL cc_start: 0.8895 (t) cc_final: 0.8638 (t) REVERT: B 743 ASN cc_start: 0.7134 (t160) cc_final: 0.6496 (t0) REVERT: B 753 LEU cc_start: 0.9002 (mt) cc_final: 0.8762 (mt) REVERT: B 779 TYR cc_start: 0.7713 (t80) cc_final: 0.6988 (t80) REVERT: B 814 ASP cc_start: 0.8862 (m-30) cc_final: 0.8628 (p0) REVERT: B 822 PHE cc_start: 0.7948 (m-80) cc_final: 0.7651 (m-80) REVERT: B 826 ASN cc_start: 0.8679 (p0) cc_final: 0.8394 (p0) REVERT: B 828 MET cc_start: 0.7791 (tmm) cc_final: 0.7244 (tpt) REVERT: B 829 ASP cc_start: 0.8323 (t0) cc_final: 0.7539 (t0) REVERT: B 841 ARG cc_start: 0.8324 (ptm160) cc_final: 0.7857 (ptm160) REVERT: B 848 ARG cc_start: 0.8656 (tmt170) cc_final: 0.8357 (tpp80) REVERT: B 859 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8237 (mtmt) REVERT: B 889 ILE cc_start: 0.8966 (pt) cc_final: 0.8754 (pt) REVERT: B 927 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7546 (tpt90) REVERT: B 946 GLU cc_start: 0.8699 (tp30) cc_final: 0.8229 (tp30) REVERT: B 1027 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8927 (mttt) REVERT: B 1036 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 1054 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 1058 ASP cc_start: 0.8814 (m-30) cc_final: 0.8170 (m-30) REVERT: B 1066 LEU cc_start: 0.9198 (mm) cc_final: 0.8986 (mm) REVERT: C 29 PHE cc_start: 0.8613 (m-80) cc_final: 0.8013 (m-10) REVERT: C 66 VAL cc_start: 0.8910 (t) cc_final: 0.7817 (m) REVERT: C 222 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8593 (mtmm) REVERT: C 326 ASP cc_start: 0.5992 (t0) cc_final: 0.5114 (p0) REVERT: C 389 MET cc_start: 0.8496 (tpt) cc_final: 0.8205 (tpt) REVERT: C 401 ASP cc_start: 0.8053 (t0) cc_final: 0.7829 (t0) REVERT: C 460 TYR cc_start: 0.8061 (t80) cc_final: 0.7669 (t80) REVERT: C 477 LEU cc_start: 0.9538 (mt) cc_final: 0.9290 (mt) REVERT: C 520 GLN cc_start: 0.8897 (mm110) cc_final: 0.7986 (mm110) REVERT: C 570 MET cc_start: 0.9067 (tpp) cc_final: 0.8443 (tpp) REVERT: C 572 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 633 TYR cc_start: 0.7882 (m-80) cc_final: 0.7654 (m-80) REVERT: C 678 MET cc_start: 0.6777 (pmm) cc_final: 0.6283 (pmm) REVERT: C 750 GLU cc_start: 0.8916 (pm20) cc_final: 0.8691 (mp0) REVERT: C 756 MET cc_start: 0.9051 (mmm) cc_final: 0.8574 (tmm) REVERT: C 763 PHE cc_start: 0.8716 (m-10) cc_final: 0.8423 (m-80) REVERT: C 791 GLN cc_start: 0.8913 (tt0) cc_final: 0.8594 (tt0) REVERT: C 794 PHE cc_start: 0.9050 (m-10) cc_final: 0.8460 (m-10) REVERT: C 806 TYR cc_start: 0.8091 (m-10) cc_final: 0.7177 (m-80) REVERT: C 816 PHE cc_start: 0.9320 (p90) cc_final: 0.9099 (p90) REVERT: C 835 LEU cc_start: 0.8638 (tp) cc_final: 0.8386 (tp) REVERT: C 875 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6717 (mt-10) REVERT: C 878 PHE cc_start: 0.8909 (m-80) cc_final: 0.7262 (m-80) REVERT: C 894 ASN cc_start: 0.9030 (t0) cc_final: 0.8458 (t0) REVERT: C 922 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8920 (tm-30) REVERT: C 925 ILE cc_start: 0.9261 (mp) cc_final: 0.9035 (mp) REVERT: C 926 ASN cc_start: 0.8973 (t0) cc_final: 0.8468 (t0) REVERT: C 939 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 945 GLU cc_start: 0.8308 (tt0) cc_final: 0.7497 (tt0) REVERT: C 949 ASP cc_start: 0.9061 (m-30) cc_final: 0.8858 (m-30) REVERT: C 959 PHE cc_start: 0.8689 (m-10) cc_final: 0.8407 (m-80) REVERT: C 962 ILE cc_start: 0.9114 (mm) cc_final: 0.8896 (mm) REVERT: C 964 GLU cc_start: 0.8270 (tp30) cc_final: 0.7956 (tp30) REVERT: C 977 GLN cc_start: 0.8955 (mp10) cc_final: 0.8456 (mp10) REVERT: C 989 GLU cc_start: 0.8642 (tp30) cc_final: 0.8414 (tp30) REVERT: C 1007 ASN cc_start: 0.9022 (m110) cc_final: 0.8520 (p0) REVERT: C 1021 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6734 (ttt90) REVERT: C 1025 ASP cc_start: 0.8311 (m-30) cc_final: 0.8050 (m-30) REVERT: C 1051 ARG cc_start: 0.7147 (ttt180) cc_final: 0.6742 (ttt180) REVERT: C 1060 ARG cc_start: 0.7400 (mmt180) cc_final: 0.6555 (mmp80) REVERT: C 1084 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8269 (mt-10) outliers start: 0 outliers final: 0 residues processed: 930 average time/residue: 0.1967 time to fit residues: 274.6334 Evaluate side-chains 851 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 851 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 247 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 232 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 395 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN ** C 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 ASN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077893 restraints weight = 78446.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080856 restraints weight = 47220.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082954 restraints weight = 31591.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084455 restraints weight = 22644.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085511 restraints weight = 17172.822| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25106 Z= 0.183 Angle : 0.685 9.411 34022 Z= 0.361 Chirality : 0.044 0.163 3789 Planarity : 0.006 0.188 4530 Dihedral : 6.562 130.425 3573 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.04 % Allowed : 1.20 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.58 (0.14), residues: 3210 helix: 0.68 (0.12), residues: 1626 sheet: -0.62 (0.30), residues: 300 loop : -1.71 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 622 TYR 0.035 0.002 TYR C 93 PHE 0.062 0.002 PHE A 611 TRP 0.013 0.002 TRP B 843 HIS 0.009 0.001 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00384 (25106) covalent geometry : angle 0.68491 (34022) hydrogen bonds : bond 0.04411 ( 1267) hydrogen bonds : angle 4.83020 ( 3678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 927 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7567 (mp0) cc_final: 0.7338 (mp0) REVERT: A 60 LEU cc_start: 0.8484 (pp) cc_final: 0.8181 (pp) REVERT: A 75 GLN cc_start: 0.9001 (mt0) cc_final: 0.8519 (mp10) REVERT: A 92 GLU cc_start: 0.9023 (mp0) cc_final: 0.8633 (pm20) REVERT: A 122 ASP cc_start: 0.8378 (t0) cc_final: 0.7818 (p0) REVERT: A 144 MET cc_start: 0.3390 (ttt) cc_final: 0.2216 (ttp) REVERT: A 182 GLN cc_start: 0.9280 (mt0) cc_final: 0.8493 (tp40) REVERT: A 222 LYS cc_start: 0.8506 (ptpp) cc_final: 0.7997 (ptpp) REVERT: A 232 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8738 (mmt90) REVERT: A 241 LEU cc_start: 0.9031 (mt) cc_final: 0.8806 (mm) REVERT: A 243 ILE cc_start: 0.9142 (mt) cc_final: 0.8876 (mp) REVERT: A 254 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8155 (ttpt) REVERT: A 273 ASN cc_start: 0.8888 (m110) cc_final: 0.8118 (t0) REVERT: A 292 LEU cc_start: 0.9259 (tp) cc_final: 0.9056 (tt) REVERT: A 306 LEU cc_start: 0.9072 (tp) cc_final: 0.8829 (tp) REVERT: A 368 TRP cc_start: 0.8976 (t60) cc_final: 0.8488 (t60) REVERT: A 376 GLN cc_start: 0.9166 (tt0) cc_final: 0.8367 (tp-100) REVERT: A 381 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8133 (tm-30) REVERT: A 389 MET cc_start: 0.8535 (tpt) cc_final: 0.8206 (tpt) REVERT: A 401 ASP cc_start: 0.8398 (t0) cc_final: 0.8000 (t0) REVERT: A 452 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8863 (mt-10) REVERT: A 470 LEU cc_start: 0.9073 (mt) cc_final: 0.8744 (mt) REVERT: A 475 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8501 (tp-100) REVERT: A 500 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9002 (tm-30) REVERT: A 515 MET cc_start: 0.9081 (mmt) cc_final: 0.8008 (mmm) REVERT: A 518 GLN cc_start: 0.9214 (mp10) cc_final: 0.8980 (mp10) REVERT: A 519 MET cc_start: 0.8782 (mmt) cc_final: 0.8191 (mmt) REVERT: A 565 ILE cc_start: 0.9162 (tp) cc_final: 0.8875 (tp) REVERT: A 660 MET cc_start: 0.8324 (ttt) cc_final: 0.7914 (ttt) REVERT: A 667 PHE cc_start: 0.8960 (m-80) cc_final: 0.8686 (m-80) REVERT: A 690 MET cc_start: 0.9029 (mtm) cc_final: 0.8554 (mtm) REVERT: A 700 ILE cc_start: 0.8926 (mm) cc_final: 0.8648 (pt) REVERT: A 720 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8400 (ttm110) REVERT: A 724 LEU cc_start: 0.9407 (mm) cc_final: 0.9154 (mm) REVERT: A 725 GLN cc_start: 0.8545 (mt0) cc_final: 0.8219 (mm-40) REVERT: A 739 ASP cc_start: 0.8687 (t70) cc_final: 0.8450 (t0) REVERT: A 747 PHE cc_start: 0.8820 (m-80) cc_final: 0.8373 (m-10) REVERT: A 750 GLU cc_start: 0.9008 (pm20) cc_final: 0.8394 (pt0) REVERT: A 753 LEU cc_start: 0.9137 (mt) cc_final: 0.8917 (mt) REVERT: A 756 MET cc_start: 0.8400 (mmp) cc_final: 0.8035 (mmp) REVERT: A 761 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 794 PHE cc_start: 0.8960 (m-80) cc_final: 0.8708 (m-80) REVERT: A 798 ASN cc_start: 0.9378 (m-40) cc_final: 0.9143 (m110) REVERT: A 804 GLU cc_start: 0.7960 (pt0) cc_final: 0.7668 (pt0) REVERT: A 824 PHE cc_start: 0.9128 (p90) cc_final: 0.8453 (p90) REVERT: A 837 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8087 (mmm-85) REVERT: A 841 ARG cc_start: 0.9212 (ttm170) cc_final: 0.8530 (ttt180) REVERT: A 842 ILE cc_start: 0.9061 (mt) cc_final: 0.8606 (tp) REVERT: A 843 TRP cc_start: 0.8791 (t-100) cc_final: 0.8463 (t-100) REVERT: A 847 MET cc_start: 0.8381 (mmm) cc_final: 0.8084 (mmt) REVERT: A 882 ARG cc_start: 0.8644 (ptm-80) cc_final: 0.7875 (ptt180) REVERT: A 894 ASN cc_start: 0.9007 (t0) cc_final: 0.8550 (t0) REVERT: A 925 ILE cc_start: 0.8750 (mm) cc_final: 0.8442 (tt) REVERT: A 943 LEU cc_start: 0.8420 (pt) cc_final: 0.8220 (pt) REVERT: A 946 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 956 LEU cc_start: 0.8892 (mm) cc_final: 0.8357 (pp) REVERT: A 959 PHE cc_start: 0.9193 (m-80) cc_final: 0.8833 (m-80) REVERT: A 962 ILE cc_start: 0.9088 (mm) cc_final: 0.8752 (mm) REVERT: A 976 TYR cc_start: 0.7918 (t80) cc_final: 0.7592 (t80) REVERT: A 980 LYS cc_start: 0.9238 (tttt) cc_final: 0.8996 (tttt) REVERT: A 1036 GLU cc_start: 0.8300 (tp30) cc_final: 0.7958 (tp30) REVERT: A 1049 LEU cc_start: 0.9342 (mt) cc_final: 0.8801 (mt) REVERT: A 1052 LEU cc_start: 0.9059 (mm) cc_final: 0.8739 (mm) REVERT: A 1058 ASP cc_start: 0.7592 (m-30) cc_final: 0.7307 (m-30) REVERT: A 1068 ASP cc_start: 0.9237 (m-30) cc_final: 0.8816 (p0) REVERT: A 1084 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 68 GLU cc_start: 0.7597 (tp30) cc_final: 0.7221 (tp30) REVERT: B 75 GLN cc_start: 0.9098 (tt0) cc_final: 0.8627 (tt0) REVERT: B 77 ASP cc_start: 0.8265 (t70) cc_final: 0.7936 (t70) REVERT: B 127 LEU cc_start: 0.9002 (mt) cc_final: 0.8680 (mt) REVERT: B 155 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9035 (mm-40) REVERT: B 178 ARG cc_start: 0.9114 (tpt-90) cc_final: 0.8740 (tpt-90) REVERT: B 200 LEU cc_start: 0.9113 (mm) cc_final: 0.8841 (tp) REVERT: B 228 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8446 (mm-30) REVERT: B 266 MET cc_start: 0.8307 (pmm) cc_final: 0.8066 (pmm) REVERT: B 275 PHE cc_start: 0.8266 (t80) cc_final: 0.7973 (t80) REVERT: B 300 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8688 (mtpt) REVERT: B 336 PHE cc_start: 0.8058 (p90) cc_final: 0.7446 (p90) REVERT: B 345 ILE cc_start: 0.8793 (mt) cc_final: 0.8315 (mt) REVERT: B 348 LEU cc_start: 0.9454 (mt) cc_final: 0.9241 (mt) REVERT: B 356 ILE cc_start: 0.8608 (mp) cc_final: 0.8018 (tt) REVERT: B 365 GLN cc_start: 0.9196 (mp10) cc_final: 0.8815 (mp10) REVERT: B 389 MET cc_start: 0.8217 (mmp) cc_final: 0.7675 (mmm) REVERT: B 448 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7867 (mtt90) REVERT: B 449 TYR cc_start: 0.9116 (p90) cc_final: 0.8873 (p90) REVERT: B 460 TYR cc_start: 0.8292 (t80) cc_final: 0.7617 (t80) REVERT: B 512 LEU cc_start: 0.9558 (mm) cc_final: 0.9207 (pp) REVERT: B 528 TYR cc_start: 0.7717 (t80) cc_final: 0.7187 (t80) REVERT: B 611 PHE cc_start: 0.7160 (m-10) cc_final: 0.6671 (m-10) REVERT: B 618 MET cc_start: 0.8393 (ttm) cc_final: 0.7714 (ttt) REVERT: B 621 LYS cc_start: 0.7900 (mmpt) cc_final: 0.6817 (mmpt) REVERT: B 660 MET cc_start: 0.8729 (ttt) cc_final: 0.8382 (ttm) REVERT: B 687 ILE cc_start: 0.8608 (mm) cc_final: 0.8043 (mm) REVERT: B 688 LEU cc_start: 0.9156 (tp) cc_final: 0.8709 (tp) REVERT: B 690 MET cc_start: 0.7691 (mtm) cc_final: 0.7391 (mtm) REVERT: B 692 MET cc_start: 0.8750 (mmp) cc_final: 0.8534 (mmp) REVERT: B 697 ASP cc_start: 0.8948 (m-30) cc_final: 0.8660 (m-30) REVERT: B 704 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7931 (ttt180) REVERT: B 716 GLU cc_start: 0.8723 (tt0) cc_final: 0.8218 (tm-30) REVERT: B 746 ILE cc_start: 0.8605 (pt) cc_final: 0.7970 (pt) REVERT: B 753 LEU cc_start: 0.8978 (mt) cc_final: 0.8742 (mt) REVERT: B 755 VAL cc_start: 0.9555 (t) cc_final: 0.9101 (t) REVERT: B 756 MET cc_start: 0.9110 (mmp) cc_final: 0.8718 (mmp) REVERT: B 779 TYR cc_start: 0.7705 (t80) cc_final: 0.7280 (t80) REVERT: B 796 LEU cc_start: 0.9155 (mt) cc_final: 0.8945 (mt) REVERT: B 814 ASP cc_start: 0.8916 (m-30) cc_final: 0.8562 (p0) REVERT: B 822 PHE cc_start: 0.7868 (m-80) cc_final: 0.7643 (m-80) REVERT: B 826 ASN cc_start: 0.8603 (p0) cc_final: 0.8301 (p0) REVERT: B 828 MET cc_start: 0.7807 (tmm) cc_final: 0.7506 (tmm) REVERT: B 829 ASP cc_start: 0.8346 (t0) cc_final: 0.7590 (t0) REVERT: B 841 ARG cc_start: 0.8310 (ptm160) cc_final: 0.7618 (ptm160) REVERT: B 847 MET cc_start: 0.7120 (tpt) cc_final: 0.6823 (mmm) REVERT: B 927 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7584 (tpt90) REVERT: B 946 GLU cc_start: 0.8602 (tp30) cc_final: 0.8060 (tp30) REVERT: B 980 LYS cc_start: 0.9135 (tttp) cc_final: 0.8512 (tttp) REVERT: B 1036 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 1054 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 1058 ASP cc_start: 0.8774 (m-30) cc_final: 0.8182 (m-30) REVERT: B 1066 LEU cc_start: 0.9223 (mm) cc_final: 0.8981 (mm) REVERT: C 29 PHE cc_start: 0.8630 (m-80) cc_final: 0.8048 (m-10) REVERT: C 66 VAL cc_start: 0.8883 (t) cc_final: 0.7678 (m) REVERT: C 230 ILE cc_start: 0.8818 (mm) cc_final: 0.8300 (tt) REVERT: C 248 ILE cc_start: 0.6832 (mm) cc_final: 0.6567 (tp) REVERT: C 347 MET cc_start: 0.4994 (mmt) cc_final: 0.4341 (mmt) REVERT: C 389 MET cc_start: 0.8480 (tpt) cc_final: 0.8237 (tpt) REVERT: C 395 GLN cc_start: 0.9121 (mt0) cc_final: 0.8720 (mm-40) REVERT: C 450 LEU cc_start: 0.8884 (tp) cc_final: 0.8582 (tp) REVERT: C 502 ASP cc_start: 0.8911 (m-30) cc_final: 0.8674 (m-30) REVERT: C 520 GLN cc_start: 0.8873 (mm110) cc_final: 0.7929 (mm110) REVERT: C 570 MET cc_start: 0.8930 (tpp) cc_final: 0.8466 (tpp) REVERT: C 572 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8123 (mt-10) REVERT: C 611 PHE cc_start: 0.8409 (m-10) cc_final: 0.8043 (m-80) REVERT: C 633 TYR cc_start: 0.7844 (m-80) cc_final: 0.7594 (m-80) REVERT: C 678 MET cc_start: 0.6915 (pmm) cc_final: 0.6432 (pmm) REVERT: C 724 LEU cc_start: 0.9212 (mp) cc_final: 0.8963 (mp) REVERT: C 756 MET cc_start: 0.9032 (mmm) cc_final: 0.8328 (tmm) REVERT: C 763 PHE cc_start: 0.8721 (m-10) cc_final: 0.8413 (m-80) REVERT: C 791 GLN cc_start: 0.8890 (tt0) cc_final: 0.8596 (tt0) REVERT: C 794 PHE cc_start: 0.9001 (m-10) cc_final: 0.8544 (m-10) REVERT: C 806 TYR cc_start: 0.8100 (m-10) cc_final: 0.7149 (m-80) REVERT: C 835 LEU cc_start: 0.8601 (tp) cc_final: 0.8362 (tp) REVERT: C 841 ARG cc_start: 0.8528 (ttt180) cc_final: 0.8311 (ttt90) REVERT: C 875 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 878 PHE cc_start: 0.8860 (m-80) cc_final: 0.7244 (m-80) REVERT: C 894 ASN cc_start: 0.9110 (t0) cc_final: 0.8551 (t0) REVERT: C 922 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8847 (tm-30) REVERT: C 925 ILE cc_start: 0.9278 (mp) cc_final: 0.9049 (mp) REVERT: C 945 GLU cc_start: 0.8363 (tt0) cc_final: 0.7595 (tt0) REVERT: C 949 ASP cc_start: 0.9142 (m-30) cc_final: 0.8903 (m-30) REVERT: C 955 VAL cc_start: 0.9093 (t) cc_final: 0.8869 (t) REVERT: C 964 GLU cc_start: 0.8552 (tp30) cc_final: 0.8032 (tp30) REVERT: C 1007 ASN cc_start: 0.9009 (m-40) cc_final: 0.8156 (p0) REVERT: C 1021 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6640 (ttt90) REVERT: C 1025 ASP cc_start: 0.8360 (m-30) cc_final: 0.8080 (m-30) REVERT: C 1051 ARG cc_start: 0.7272 (ttt180) cc_final: 0.6626 (ttt180) REVERT: C 1060 ARG cc_start: 0.7430 (mmt180) cc_final: 0.6883 (mmt180) REVERT: C 1063 PHE cc_start: 0.9138 (t80) cc_final: 0.8863 (t80) outliers start: 1 outliers final: 1 residues processed: 927 average time/residue: 0.1926 time to fit residues: 269.4444 Evaluate side-chains 841 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 840 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 65 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 308 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 250 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN B1028 GLN C 374 GLN C 461 HIS ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 791 GLN ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 886 GLN C 896 ASN ** C 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 ASN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078694 restraints weight = 77824.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081742 restraints weight = 46757.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083886 restraints weight = 31206.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085420 restraints weight = 22367.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086506 restraints weight = 16956.864| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25106 Z= 0.148 Angle : 0.688 10.476 34022 Z= 0.359 Chirality : 0.044 0.242 3789 Planarity : 0.006 0.155 4530 Dihedral : 6.407 125.918 3573 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.51 (0.15), residues: 3210 helix: 0.71 (0.12), residues: 1626 sheet: -0.74 (0.28), residues: 339 loop : -1.61 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 869 TYR 0.036 0.002 TYR C 93 PHE 0.036 0.002 PHE C 959 TRP 0.014 0.002 TRP B 516 HIS 0.008 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00319 (25106) covalent geometry : angle 0.68839 (34022) hydrogen bonds : bond 0.04290 ( 1267) hydrogen bonds : angle 4.70263 ( 3678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 927 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8039 (m-80) cc_final: 0.7791 (m-80) REVERT: A 56 GLU cc_start: 0.7514 (mp0) cc_final: 0.7284 (mp0) REVERT: A 75 GLN cc_start: 0.9005 (mt0) cc_final: 0.8501 (mp10) REVERT: A 92 GLU cc_start: 0.9030 (mp0) cc_final: 0.8623 (pm20) REVERT: A 122 ASP cc_start: 0.8343 (t0) cc_final: 0.7835 (p0) REVERT: A 144 MET cc_start: 0.3378 (ttt) cc_final: 0.2265 (ttp) REVERT: A 149 MET cc_start: 0.7276 (ptp) cc_final: 0.6885 (ptp) REVERT: A 182 GLN cc_start: 0.9291 (mt0) cc_final: 0.8467 (tp40) REVERT: A 222 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8045 (ptpp) REVERT: A 232 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8747 (mmt90) REVERT: A 241 LEU cc_start: 0.9053 (mt) cc_final: 0.8794 (mm) REVERT: A 243 ILE cc_start: 0.9043 (mt) cc_final: 0.8618 (mp) REVERT: A 273 ASN cc_start: 0.8874 (m110) cc_final: 0.8072 (t0) REVERT: A 292 LEU cc_start: 0.9278 (tp) cc_final: 0.8925 (tp) REVERT: A 332 MET cc_start: 0.8355 (ttm) cc_final: 0.8145 (ttm) REVERT: A 368 TRP cc_start: 0.8958 (t60) cc_final: 0.8576 (t60) REVERT: A 376 GLN cc_start: 0.9121 (tt0) cc_final: 0.8351 (tp-100) REVERT: A 381 GLN cc_start: 0.8992 (tp-100) cc_final: 0.7883 (tm-30) REVERT: A 389 MET cc_start: 0.8552 (tpt) cc_final: 0.8184 (tpt) REVERT: A 401 ASP cc_start: 0.8379 (t0) cc_final: 0.7961 (t0) REVERT: A 461 HIS cc_start: 0.8915 (m90) cc_final: 0.8704 (m90) REVERT: A 470 LEU cc_start: 0.9048 (mt) cc_final: 0.8723 (mt) REVERT: A 475 GLN cc_start: 0.8772 (tp-100) cc_final: 0.7887 (tt0) REVERT: A 500 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9014 (tm-30) REVERT: A 515 MET cc_start: 0.9056 (mmt) cc_final: 0.8598 (mmm) REVERT: A 519 MET cc_start: 0.8807 (mmt) cc_final: 0.8357 (mmm) REVERT: A 565 ILE cc_start: 0.9168 (tp) cc_final: 0.8790 (tp) REVERT: A 569 LEU cc_start: 0.8018 (mt) cc_final: 0.7808 (mt) REVERT: A 640 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6386 (mtt180) REVERT: A 654 ILE cc_start: 0.9249 (pt) cc_final: 0.9042 (pt) REVERT: A 660 MET cc_start: 0.8317 (ttt) cc_final: 0.7897 (ttt) REVERT: A 667 PHE cc_start: 0.9024 (m-80) cc_final: 0.8711 (m-80) REVERT: A 688 LEU cc_start: 0.9122 (pp) cc_final: 0.8773 (pp) REVERT: A 690 MET cc_start: 0.8983 (mtm) cc_final: 0.8551 (mtm) REVERT: A 700 ILE cc_start: 0.8911 (mm) cc_final: 0.8625 (pt) REVERT: A 720 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8376 (ttm110) REVERT: A 724 LEU cc_start: 0.9417 (mm) cc_final: 0.9145 (mm) REVERT: A 725 GLN cc_start: 0.8543 (mt0) cc_final: 0.8197 (mm-40) REVERT: A 739 ASP cc_start: 0.8802 (t70) cc_final: 0.8474 (t0) REVERT: A 747 PHE cc_start: 0.8805 (m-80) cc_final: 0.8318 (m-10) REVERT: A 750 GLU cc_start: 0.8981 (pm20) cc_final: 0.8397 (pt0) REVERT: A 753 LEU cc_start: 0.9118 (mt) cc_final: 0.8903 (mt) REVERT: A 756 MET cc_start: 0.8402 (mmp) cc_final: 0.8046 (mmp) REVERT: A 760 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8934 (tp-100) REVERT: A 761 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 794 PHE cc_start: 0.8947 (m-80) cc_final: 0.8700 (m-80) REVERT: A 798 ASN cc_start: 0.9361 (m-40) cc_final: 0.9146 (m110) REVERT: A 804 GLU cc_start: 0.7909 (pt0) cc_final: 0.7598 (pt0) REVERT: A 824 PHE cc_start: 0.9115 (p90) cc_final: 0.8389 (p90) REVERT: A 837 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8024 (mmm-85) REVERT: A 841 ARG cc_start: 0.9246 (ttm170) cc_final: 0.8555 (ttt180) REVERT: A 842 ILE cc_start: 0.9010 (mt) cc_final: 0.8572 (tp) REVERT: A 843 TRP cc_start: 0.8725 (t-100) cc_final: 0.8347 (t-100) REVERT: A 847 MET cc_start: 0.8273 (mmm) cc_final: 0.8011 (mmt) REVERT: A 882 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.7864 (ptt180) REVERT: A 894 ASN cc_start: 0.9004 (t0) cc_final: 0.8467 (t0) REVERT: A 925 ILE cc_start: 0.8707 (mm) cc_final: 0.8372 (tt) REVERT: A 946 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 959 PHE cc_start: 0.9180 (m-80) cc_final: 0.8813 (m-80) REVERT: A 962 ILE cc_start: 0.9087 (mm) cc_final: 0.8737 (mm) REVERT: A 976 TYR cc_start: 0.7870 (t80) cc_final: 0.7563 (t80) REVERT: A 980 LYS cc_start: 0.9082 (tttt) cc_final: 0.8881 (tttt) REVERT: A 1033 ARG cc_start: 0.8971 (mtp85) cc_final: 0.8645 (mtp-110) REVERT: A 1036 GLU cc_start: 0.8349 (tp30) cc_final: 0.7988 (tp30) REVERT: A 1049 LEU cc_start: 0.9363 (mt) cc_final: 0.8731 (mt) REVERT: A 1058 ASP cc_start: 0.7271 (m-30) cc_final: 0.6916 (m-30) REVERT: A 1068 ASP cc_start: 0.9278 (m-30) cc_final: 0.8509 (p0) REVERT: A 1084 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8454 (mm-30) REVERT: B 28 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8305 (mtp180) REVERT: B 75 GLN cc_start: 0.9130 (tt0) cc_final: 0.8625 (tt0) REVERT: B 77 ASP cc_start: 0.8224 (t70) cc_final: 0.7984 (t70) REVERT: B 96 TYR cc_start: 0.6878 (t80) cc_final: 0.6367 (t80) REVERT: B 102 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8624 (ttp80) REVERT: B 127 LEU cc_start: 0.8978 (mt) cc_final: 0.8665 (mt) REVERT: B 155 GLN cc_start: 0.9391 (mm-40) cc_final: 0.8986 (mm-40) REVERT: B 178 ARG cc_start: 0.9106 (tpt-90) cc_final: 0.8773 (tpt-90) REVERT: B 200 LEU cc_start: 0.9061 (mm) cc_final: 0.8788 (tp) REVERT: B 266 MET cc_start: 0.8353 (pmm) cc_final: 0.8106 (pmm) REVERT: B 275 PHE cc_start: 0.8069 (t80) cc_final: 0.7757 (t80) REVERT: B 276 MET cc_start: 0.8601 (tpt) cc_final: 0.7716 (tpp) REVERT: B 300 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8765 (mtpt) REVERT: B 314 ILE cc_start: 0.9331 (pt) cc_final: 0.9129 (pt) REVERT: B 336 PHE cc_start: 0.7908 (p90) cc_final: 0.7499 (p90) REVERT: B 345 ILE cc_start: 0.8747 (mt) cc_final: 0.8242 (mt) REVERT: B 348 LEU cc_start: 0.9420 (mt) cc_final: 0.9139 (mt) REVERT: B 356 ILE cc_start: 0.8586 (mp) cc_final: 0.7884 (tt) REVERT: B 365 GLN cc_start: 0.9205 (mp10) cc_final: 0.8808 (mp10) REVERT: B 389 MET cc_start: 0.8200 (mmp) cc_final: 0.7630 (mmm) REVERT: B 394 THR cc_start: 0.8805 (p) cc_final: 0.8563 (p) REVERT: B 402 ASP cc_start: 0.8697 (m-30) cc_final: 0.8072 (m-30) REVERT: B 408 TYR cc_start: 0.8185 (t80) cc_final: 0.7808 (t80) REVERT: B 448 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7822 (mtt90) REVERT: B 460 TYR cc_start: 0.8220 (t80) cc_final: 0.7569 (t80) REVERT: B 477 LEU cc_start: 0.8001 (pp) cc_final: 0.7765 (pp) REVERT: B 510 ARG cc_start: 0.8943 (mtp180) cc_final: 0.8184 (mtp85) REVERT: B 512 LEU cc_start: 0.9548 (mm) cc_final: 0.9200 (pp) REVERT: B 528 TYR cc_start: 0.7727 (t80) cc_final: 0.7208 (t80) REVERT: B 611 PHE cc_start: 0.7101 (m-10) cc_final: 0.6590 (m-10) REVERT: B 618 MET cc_start: 0.8403 (ttm) cc_final: 0.7666 (ttt) REVERT: B 621 LYS cc_start: 0.7842 (mmpt) cc_final: 0.6740 (mmpt) REVERT: B 660 MET cc_start: 0.8718 (ttt) cc_final: 0.8380 (ttm) REVERT: B 687 ILE cc_start: 0.8545 (mm) cc_final: 0.7979 (mm) REVERT: B 688 LEU cc_start: 0.9128 (tp) cc_final: 0.8544 (tp) REVERT: B 690 MET cc_start: 0.7642 (mtm) cc_final: 0.7353 (mtm) REVERT: B 697 ASP cc_start: 0.8943 (m-30) cc_final: 0.8638 (m-30) REVERT: B 704 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7928 (ttt180) REVERT: B 716 GLU cc_start: 0.8684 (tt0) cc_final: 0.8200 (tm-30) REVERT: B 737 LYS cc_start: 0.9447 (ptmt) cc_final: 0.8849 (ptmt) REVERT: B 743 ASN cc_start: 0.7099 (t160) cc_final: 0.6830 (t0) REVERT: B 746 ILE cc_start: 0.8611 (pt) cc_final: 0.8117 (pt) REVERT: B 753 LEU cc_start: 0.8915 (mt) cc_final: 0.8661 (mt) REVERT: B 755 VAL cc_start: 0.9548 (t) cc_final: 0.9307 (t) REVERT: B 756 MET cc_start: 0.9085 (mmp) cc_final: 0.8727 (mmp) REVERT: B 779 TYR cc_start: 0.7686 (t80) cc_final: 0.7302 (t80) REVERT: B 796 LEU cc_start: 0.9119 (mt) cc_final: 0.8096 (mt) REVERT: B 800 PHE cc_start: 0.8646 (m-10) cc_final: 0.8291 (m-10) REVERT: B 814 ASP cc_start: 0.8876 (m-30) cc_final: 0.8531 (p0) REVERT: B 822 PHE cc_start: 0.7891 (m-80) cc_final: 0.7664 (m-80) REVERT: B 826 ASN cc_start: 0.8542 (p0) cc_final: 0.8217 (p0) REVERT: B 828 MET cc_start: 0.7796 (tmm) cc_final: 0.7526 (tmm) REVERT: B 829 ASP cc_start: 0.8339 (t0) cc_final: 0.8005 (t0) REVERT: B 837 ARG cc_start: 0.9151 (mtp-110) cc_final: 0.8754 (mtp85) REVERT: B 841 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7561 (ptm160) REVERT: B 854 ASN cc_start: 0.8997 (t0) cc_final: 0.8731 (t0) REVERT: B 858 GLN cc_start: 0.9120 (pp30) cc_final: 0.8864 (pp30) REVERT: B 889 ILE cc_start: 0.8989 (pt) cc_final: 0.8745 (pt) REVERT: B 945 GLU cc_start: 0.7948 (pm20) cc_final: 0.7675 (mp0) REVERT: B 946 GLU cc_start: 0.8630 (tp30) cc_final: 0.7572 (tp30) REVERT: B 980 LYS cc_start: 0.9138 (tttp) cc_final: 0.8520 (tttp) REVERT: B 1027 LYS cc_start: 0.9262 (mtmm) cc_final: 0.9021 (mttt) REVERT: B 1036 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8654 (mt-10) REVERT: B 1054 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 1058 ASP cc_start: 0.8742 (m-30) cc_final: 0.8234 (m-30) REVERT: B 1066 LEU cc_start: 0.9207 (mm) cc_final: 0.8967 (mm) REVERT: C 29 PHE cc_start: 0.8575 (m-80) cc_final: 0.8012 (m-10) REVERT: C 64 ARG cc_start: 0.7554 (mmp80) cc_final: 0.7143 (mmm160) REVERT: C 66 VAL cc_start: 0.8895 (t) cc_final: 0.7722 (m) REVERT: C 153 MET cc_start: 0.7818 (mmm) cc_final: 0.7519 (mmm) REVERT: C 227 ASP cc_start: 0.8326 (t0) cc_final: 0.8115 (t0) REVERT: C 230 ILE cc_start: 0.8847 (mm) cc_final: 0.8390 (tt) REVERT: C 248 ILE cc_start: 0.6804 (mm) cc_final: 0.6507 (tp) REVERT: C 292 LEU cc_start: 0.6537 (mp) cc_final: 0.6192 (mt) REVERT: C 347 MET cc_start: 0.4962 (mmt) cc_final: 0.4296 (mmt) REVERT: C 389 MET cc_start: 0.8529 (tpt) cc_final: 0.8267 (tpt) REVERT: C 520 GLN cc_start: 0.8678 (mm110) cc_final: 0.7782 (mm110) REVERT: C 570 MET cc_start: 0.8946 (tpp) cc_final: 0.8615 (tpp) REVERT: C 572 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8097 (mt-10) REVERT: C 573 ASN cc_start: 0.9295 (t0) cc_final: 0.8074 (m-40) REVERT: C 611 PHE cc_start: 0.8388 (m-10) cc_final: 0.8027 (m-80) REVERT: C 632 LEU cc_start: 0.7494 (tt) cc_final: 0.7003 (mm) REVERT: C 633 TYR cc_start: 0.7806 (m-80) cc_final: 0.7527 (m-80) REVERT: C 678 MET cc_start: 0.6951 (pmm) cc_final: 0.6463 (pmm) REVERT: C 692 MET cc_start: 0.8795 (mpp) cc_final: 0.8443 (mpp) REVERT: C 756 MET cc_start: 0.9051 (mmm) cc_final: 0.8346 (tmm) REVERT: C 763 PHE cc_start: 0.8724 (m-10) cc_final: 0.8396 (m-10) REVERT: C 794 PHE cc_start: 0.8962 (m-10) cc_final: 0.8550 (m-10) REVERT: C 806 TYR cc_start: 0.8025 (m-10) cc_final: 0.6997 (m-80) REVERT: C 826 ASN cc_start: 0.8001 (m110) cc_final: 0.7730 (m110) REVERT: C 835 LEU cc_start: 0.8574 (tp) cc_final: 0.8343 (tp) REVERT: C 841 ARG cc_start: 0.8666 (ttt180) cc_final: 0.8341 (ttt90) REVERT: C 875 GLU cc_start: 0.7566 (mt-10) cc_final: 0.6795 (mt-10) REVERT: C 878 PHE cc_start: 0.8867 (m-80) cc_final: 0.7310 (m-80) REVERT: C 886 GLN cc_start: 0.9018 (tp40) cc_final: 0.8727 (tp40) REVERT: C 894 ASN cc_start: 0.9156 (t0) cc_final: 0.8583 (t0) REVERT: C 922 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 925 ILE cc_start: 0.9290 (mp) cc_final: 0.9073 (mp) REVERT: C 939 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 945 GLU cc_start: 0.8703 (tt0) cc_final: 0.8367 (tt0) REVERT: C 949 ASP cc_start: 0.9174 (m-30) cc_final: 0.8949 (m-30) REVERT: C 955 VAL cc_start: 0.9145 (t) cc_final: 0.8894 (p) REVERT: C 959 PHE cc_start: 0.8802 (m-80) cc_final: 0.8498 (m-80) REVERT: C 964 GLU cc_start: 0.8462 (tp30) cc_final: 0.8003 (tp30) REVERT: C 1007 ASN cc_start: 0.9042 (m-40) cc_final: 0.8271 (p0) REVERT: C 1021 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6726 (ttt90) REVERT: C 1025 ASP cc_start: 0.8396 (m-30) cc_final: 0.8131 (m-30) REVERT: C 1030 GLN cc_start: 0.8861 (mp10) cc_final: 0.8408 (mp10) REVERT: C 1051 ARG cc_start: 0.7373 (ttt180) cc_final: 0.6710 (ttt180) REVERT: C 1060 ARG cc_start: 0.7379 (mmt180) cc_final: 0.6875 (mmt180) REVERT: C 1063 PHE cc_start: 0.9123 (t80) cc_final: 0.8706 (t80) REVERT: C 1088 GLN cc_start: 0.8039 (pm20) cc_final: 0.7675 (pp30) outliers start: 0 outliers final: 0 residues processed: 927 average time/residue: 0.1951 time to fit residues: 272.4158 Evaluate side-chains 848 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 848 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 39 optimal weight: 0.6980 chunk 271 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 249 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 273 optimal weight: 0.5980 chunk 289 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 573 ASN A 780 HIS ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN ** B 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN C 374 GLN ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 HIS C 896 ASN ** C 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081110 restraints weight = 76877.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084237 restraints weight = 45948.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086442 restraints weight = 30604.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088044 restraints weight = 21878.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089154 restraints weight = 16518.086| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25106 Z= 0.132 Angle : 0.681 10.644 34022 Z= 0.350 Chirality : 0.044 0.337 3789 Planarity : 0.005 0.111 4530 Dihedral : 6.128 125.405 3573 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.32 (0.15), residues: 3210 helix: 0.83 (0.13), residues: 1638 sheet: -0.52 (0.30), residues: 288 loop : -1.48 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 869 TYR 0.039 0.002 TYR C 93 PHE 0.039 0.002 PHE A 233 TRP 0.030 0.002 TRP A 568 HIS 0.009 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00286 (25106) covalent geometry : angle 0.68109 (34022) hydrogen bonds : bond 0.03986 ( 1267) hydrogen bonds : angle 4.51553 ( 3678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 931 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7446 (mp0) cc_final: 0.7206 (mp0) REVERT: A 92 GLU cc_start: 0.9006 (mp0) cc_final: 0.8769 (pm20) REVERT: A 97 MET cc_start: 0.9103 (mtt) cc_final: 0.8606 (mtm) REVERT: A 122 ASP cc_start: 0.8390 (t0) cc_final: 0.7992 (p0) REVERT: A 144 MET cc_start: 0.3240 (ttt) cc_final: 0.2225 (ttp) REVERT: A 180 LEU cc_start: 0.8893 (tp) cc_final: 0.8691 (tp) REVERT: A 182 GLN cc_start: 0.9280 (mt0) cc_final: 0.8417 (tp40) REVERT: A 222 LYS cc_start: 0.8569 (ptpp) cc_final: 0.7983 (ptpp) REVERT: A 230 ILE cc_start: 0.9138 (mt) cc_final: 0.8935 (mt) REVERT: A 232 ARG cc_start: 0.8979 (mmt90) cc_final: 0.8589 (mmt90) REVERT: A 241 LEU cc_start: 0.9116 (mt) cc_final: 0.8789 (mm) REVERT: A 243 ILE cc_start: 0.8873 (mt) cc_final: 0.8390 (mp) REVERT: A 253 ARG cc_start: 0.8057 (tpt90) cc_final: 0.7797 (tpt90) REVERT: A 273 ASN cc_start: 0.8801 (m110) cc_final: 0.7919 (t0) REVERT: A 292 LEU cc_start: 0.9350 (tp) cc_final: 0.9020 (tp) REVERT: A 306 LEU cc_start: 0.8960 (tp) cc_final: 0.8686 (mm) REVERT: A 346 ASP cc_start: 0.8222 (m-30) cc_final: 0.7709 (m-30) REVERT: A 376 GLN cc_start: 0.8891 (tt0) cc_final: 0.8153 (tp40) REVERT: A 381 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8000 (tm-30) REVERT: A 389 MET cc_start: 0.8633 (tpt) cc_final: 0.8152 (tpt) REVERT: A 401 ASP cc_start: 0.8384 (t0) cc_final: 0.7727 (t0) REVERT: A 470 LEU cc_start: 0.9084 (mt) cc_final: 0.8795 (mt) REVERT: A 482 ASP cc_start: 0.9083 (m-30) cc_final: 0.8833 (m-30) REVERT: A 497 LEU cc_start: 0.9351 (mt) cc_final: 0.9092 (pp) REVERT: A 500 GLU cc_start: 0.9533 (tm-30) cc_final: 0.8999 (tm-30) REVERT: A 515 MET cc_start: 0.9037 (mmt) cc_final: 0.8738 (mmm) REVERT: A 518 GLN cc_start: 0.9187 (mp10) cc_final: 0.8976 (mp10) REVERT: A 519 MET cc_start: 0.8606 (mmt) cc_final: 0.8320 (mmm) REVERT: A 565 ILE cc_start: 0.9173 (tp) cc_final: 0.8783 (tp) REVERT: A 608 ASN cc_start: 0.8579 (m-40) cc_final: 0.8318 (m-40) REVERT: A 654 ILE cc_start: 0.9206 (pt) cc_final: 0.8990 (pt) REVERT: A 660 MET cc_start: 0.8225 (ttt) cc_final: 0.7813 (ttt) REVERT: A 667 PHE cc_start: 0.8977 (m-80) cc_final: 0.8695 (m-80) REVERT: A 700 ILE cc_start: 0.8845 (mm) cc_final: 0.8582 (pt) REVERT: A 720 ARG cc_start: 0.8582 (mtp-110) cc_final: 0.8259 (ttm110) REVERT: A 724 LEU cc_start: 0.9576 (mm) cc_final: 0.9147 (mm) REVERT: A 725 GLN cc_start: 0.8508 (mt0) cc_final: 0.8214 (mm-40) REVERT: A 739 ASP cc_start: 0.8727 (t70) cc_final: 0.8317 (t0) REVERT: A 747 PHE cc_start: 0.8788 (m-80) cc_final: 0.8358 (m-10) REVERT: A 750 GLU cc_start: 0.8958 (pm20) cc_final: 0.8347 (pt0) REVERT: A 756 MET cc_start: 0.8396 (mmp) cc_final: 0.8028 (mmp) REVERT: A 761 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 794 PHE cc_start: 0.8900 (m-80) cc_final: 0.8610 (m-10) REVERT: A 800 PHE cc_start: 0.9048 (m-80) cc_final: 0.8711 (m-80) REVERT: A 814 ASP cc_start: 0.8857 (p0) cc_final: 0.8653 (p0) REVERT: A 837 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7911 (mmm-85) REVERT: A 841 ARG cc_start: 0.9126 (ttm170) cc_final: 0.8728 (ttp80) REVERT: A 842 ILE cc_start: 0.8961 (mt) cc_final: 0.8549 (tp) REVERT: A 843 TRP cc_start: 0.8717 (t-100) cc_final: 0.8177 (t-100) REVERT: A 847 MET cc_start: 0.8133 (mmm) cc_final: 0.7915 (mmt) REVERT: A 882 ARG cc_start: 0.8659 (ptm-80) cc_final: 0.7886 (ptt180) REVERT: A 894 ASN cc_start: 0.8956 (t0) cc_final: 0.8056 (p0) REVERT: A 896 ASN cc_start: 0.8993 (m110) cc_final: 0.8780 (m110) REVERT: A 925 ILE cc_start: 0.8657 (mm) cc_final: 0.8301 (tt) REVERT: A 943 LEU cc_start: 0.8101 (pt) cc_final: 0.7750 (pt) REVERT: A 946 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 959 PHE cc_start: 0.9104 (m-80) cc_final: 0.8808 (m-80) REVERT: A 962 ILE cc_start: 0.9046 (mm) cc_final: 0.8737 (mm) REVERT: A 977 GLN cc_start: 0.8934 (mp10) cc_final: 0.8640 (mp10) REVERT: A 980 LYS cc_start: 0.8996 (tttt) cc_final: 0.8773 (tttt) REVERT: A 1033 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8672 (mtp-110) REVERT: A 1036 GLU cc_start: 0.8314 (tp30) cc_final: 0.7941 (tp30) REVERT: A 1049 LEU cc_start: 0.9153 (mt) cc_final: 0.8758 (mt) REVERT: A 1058 ASP cc_start: 0.6777 (m-30) cc_final: 0.6345 (m-30) REVERT: A 1068 ASP cc_start: 0.9301 (m-30) cc_final: 0.8586 (p0) REVERT: A 1084 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8485 (mm-30) REVERT: B 28 ARG cc_start: 0.8634 (mtp180) cc_final: 0.8376 (mtp180) REVERT: B 68 GLU cc_start: 0.7518 (tp30) cc_final: 0.7214 (tp30) REVERT: B 75 GLN cc_start: 0.9098 (tt0) cc_final: 0.8672 (tt0) REVERT: B 77 ASP cc_start: 0.8214 (t70) cc_final: 0.7984 (t70) REVERT: B 102 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8505 (ttp80) REVERT: B 127 LEU cc_start: 0.8903 (mt) cc_final: 0.8577 (mt) REVERT: B 178 ARG cc_start: 0.9077 (tpt-90) cc_final: 0.8842 (tpt-90) REVERT: B 180 LEU cc_start: 0.9036 (tp) cc_final: 0.8831 (tp) REVERT: B 189 ASN cc_start: 0.7314 (t0) cc_final: 0.6967 (p0) REVERT: B 200 LEU cc_start: 0.9018 (mm) cc_final: 0.8768 (tp) REVERT: B 266 MET cc_start: 0.8358 (pmm) cc_final: 0.8015 (pmm) REVERT: B 275 PHE cc_start: 0.7801 (t80) cc_final: 0.7511 (t80) REVERT: B 276 MET cc_start: 0.8515 (tpt) cc_final: 0.7682 (tpp) REVERT: B 292 LEU cc_start: 0.9076 (tt) cc_final: 0.8737 (mt) REVERT: B 300 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8852 (mtpt) REVERT: B 336 PHE cc_start: 0.7888 (p90) cc_final: 0.7448 (p90) REVERT: B 345 ILE cc_start: 0.8697 (mt) cc_final: 0.8386 (mm) REVERT: B 356 ILE cc_start: 0.8479 (mp) cc_final: 0.7853 (tt) REVERT: B 362 LYS cc_start: 0.8669 (mptt) cc_final: 0.8419 (mptt) REVERT: B 365 GLN cc_start: 0.9218 (mp10) cc_final: 0.8799 (mp10) REVERT: B 389 MET cc_start: 0.8133 (mmp) cc_final: 0.7593 (mmm) REVERT: B 394 THR cc_start: 0.8649 (p) cc_final: 0.8402 (p) REVERT: B 408 TYR cc_start: 0.8152 (t80) cc_final: 0.7771 (t80) REVERT: B 448 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7894 (mtt90) REVERT: B 460 TYR cc_start: 0.8066 (t80) cc_final: 0.7437 (t80) REVERT: B 474 ARG cc_start: 0.8365 (tpt-90) cc_final: 0.7804 (tpt-90) REVERT: B 477 LEU cc_start: 0.8056 (pp) cc_final: 0.7059 (pp) REVERT: B 501 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7952 (tmm160) REVERT: B 510 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8099 (mtp85) REVERT: B 512 LEU cc_start: 0.9536 (mm) cc_final: 0.9190 (pp) REVERT: B 528 TYR cc_start: 0.7675 (t80) cc_final: 0.7170 (t80) REVERT: B 611 PHE cc_start: 0.7060 (m-10) cc_final: 0.6577 (m-10) REVERT: B 618 MET cc_start: 0.8121 (ttm) cc_final: 0.7394 (ttt) REVERT: B 621 LYS cc_start: 0.7787 (mmpt) cc_final: 0.6700 (mmpt) REVERT: B 687 ILE cc_start: 0.8497 (mm) cc_final: 0.7747 (mm) REVERT: B 688 LEU cc_start: 0.9321 (tp) cc_final: 0.8561 (tp) REVERT: B 690 MET cc_start: 0.7645 (mtm) cc_final: 0.7420 (mtm) REVERT: B 697 ASP cc_start: 0.8922 (m-30) cc_final: 0.8589 (m-30) REVERT: B 716 GLU cc_start: 0.8627 (tt0) cc_final: 0.8105 (tm-30) REVERT: B 737 LYS cc_start: 0.9403 (ptmt) cc_final: 0.8857 (ptmt) REVERT: B 755 VAL cc_start: 0.9524 (t) cc_final: 0.9278 (t) REVERT: B 779 TYR cc_start: 0.7689 (t80) cc_final: 0.7262 (t80) REVERT: B 796 LEU cc_start: 0.9076 (mt) cc_final: 0.8110 (mt) REVERT: B 800 PHE cc_start: 0.8376 (m-10) cc_final: 0.7617 (m-10) REVERT: B 814 ASP cc_start: 0.8874 (m-30) cc_final: 0.8519 (p0) REVERT: B 815 ASP cc_start: 0.8519 (m-30) cc_final: 0.8137 (m-30) REVERT: B 826 ASN cc_start: 0.8539 (p0) cc_final: 0.8238 (p0) REVERT: B 828 MET cc_start: 0.7743 (tmm) cc_final: 0.7489 (tmm) REVERT: B 831 GLU cc_start: 0.8927 (mp0) cc_final: 0.8699 (mp0) REVERT: B 837 ARG cc_start: 0.9113 (mtp-110) cc_final: 0.8680 (mtp85) REVERT: B 841 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7681 (ptm160) REVERT: B 854 ASN cc_start: 0.8901 (t0) cc_final: 0.8623 (t0) REVERT: B 858 GLN cc_start: 0.9131 (pp30) cc_final: 0.8897 (pp30) REVERT: B 945 GLU cc_start: 0.7942 (pm20) cc_final: 0.7692 (mp0) REVERT: B 946 GLU cc_start: 0.8551 (tp30) cc_final: 0.7779 (tp30) REVERT: B 980 LYS cc_start: 0.9145 (tttp) cc_final: 0.8536 (tttp) REVERT: B 1036 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 1054 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 1058 ASP cc_start: 0.8675 (m-30) cc_final: 0.8167 (m-30) REVERT: B 1067 MET cc_start: 0.8337 (mmp) cc_final: 0.8060 (mmt) REVERT: B 1068 ASP cc_start: 0.8446 (m-30) cc_final: 0.8013 (t0) REVERT: B 1091 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7932 (mmt90) REVERT: C 29 PHE cc_start: 0.8418 (m-80) cc_final: 0.7856 (m-10) REVERT: C 30 VAL cc_start: 0.7053 (p) cc_final: 0.6703 (m) REVERT: C 64 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7478 (mmm160) REVERT: C 66 VAL cc_start: 0.8906 (t) cc_final: 0.7986 (m) REVERT: C 96 TYR cc_start: 0.8674 (t80) cc_final: 0.8460 (t80) REVERT: C 153 MET cc_start: 0.7706 (mmm) cc_final: 0.7471 (mmm) REVERT: C 230 ILE cc_start: 0.8822 (mm) cc_final: 0.8365 (tt) REVERT: C 292 LEU cc_start: 0.6476 (mp) cc_final: 0.6116 (mt) REVERT: C 347 MET cc_start: 0.4792 (mmt) cc_final: 0.4151 (mmt) REVERT: C 389 MET cc_start: 0.8537 (tpt) cc_final: 0.8268 (tpt) REVERT: C 395 GLN cc_start: 0.8673 (mt0) cc_final: 0.8325 (mm-40) REVERT: C 450 LEU cc_start: 0.8399 (tp) cc_final: 0.8155 (tp) REVERT: C 502 ASP cc_start: 0.8878 (m-30) cc_final: 0.8658 (m-30) REVERT: C 515 MET cc_start: 0.8890 (mmp) cc_final: 0.8509 (mmp) REVERT: C 520 GLN cc_start: 0.8637 (mm110) cc_final: 0.7702 (mm110) REVERT: C 570 MET cc_start: 0.8966 (tpp) cc_final: 0.8440 (tpp) REVERT: C 572 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 573 ASN cc_start: 0.9284 (t0) cc_final: 0.8850 (t0) REVERT: C 588 LYS cc_start: 0.9202 (tptp) cc_final: 0.8823 (tptt) REVERT: C 611 PHE cc_start: 0.8329 (m-10) cc_final: 0.7988 (m-80) REVERT: C 633 TYR cc_start: 0.7766 (m-80) cc_final: 0.7453 (m-80) REVERT: C 678 MET cc_start: 0.6879 (pmm) cc_final: 0.6463 (pmm) REVERT: C 688 LEU cc_start: 0.7169 (tp) cc_final: 0.6693 (tp) REVERT: C 692 MET cc_start: 0.8848 (mpp) cc_final: 0.8246 (mpp) REVERT: C 726 ASN cc_start: 0.8356 (m110) cc_final: 0.8118 (m110) REVERT: C 750 GLU cc_start: 0.8536 (mp0) cc_final: 0.7555 (pm20) REVERT: C 753 LEU cc_start: 0.8533 (mt) cc_final: 0.8316 (mt) REVERT: C 754 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7725 (mmtt) REVERT: C 756 MET cc_start: 0.9018 (mmm) cc_final: 0.8777 (tmm) REVERT: C 763 PHE cc_start: 0.8661 (m-10) cc_final: 0.8344 (m-10) REVERT: C 794 PHE cc_start: 0.8939 (m-10) cc_final: 0.8619 (m-10) REVERT: C 806 TYR cc_start: 0.8019 (m-10) cc_final: 0.7566 (m-80) REVERT: C 824 PHE cc_start: 0.8436 (p90) cc_final: 0.8126 (p90) REVERT: C 835 LEU cc_start: 0.8352 (tp) cc_final: 0.8093 (tp) REVERT: C 837 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.7531 (tpp80) REVERT: C 894 ASN cc_start: 0.9189 (t0) cc_final: 0.8559 (t0) REVERT: C 925 ILE cc_start: 0.9279 (mp) cc_final: 0.9072 (mp) REVERT: C 939 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 955 VAL cc_start: 0.9041 (t) cc_final: 0.8839 (p) REVERT: C 959 PHE cc_start: 0.8779 (m-80) cc_final: 0.8533 (m-80) REVERT: C 1007 ASN cc_start: 0.9053 (m-40) cc_final: 0.8128 (p0) REVERT: C 1021 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6782 (ttt-90) REVERT: C 1025 ASP cc_start: 0.8357 (m-30) cc_final: 0.8086 (m-30) REVERT: C 1030 GLN cc_start: 0.8895 (mp10) cc_final: 0.8527 (mp10) REVERT: C 1048 MET cc_start: 0.8641 (mmm) cc_final: 0.7464 (mtt) REVERT: C 1060 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6748 (mmt180) REVERT: C 1063 PHE cc_start: 0.9002 (t80) cc_final: 0.8649 (t80) REVERT: C 1088 GLN cc_start: 0.7905 (pm20) cc_final: 0.7547 (pp30) outliers start: 0 outliers final: 0 residues processed: 931 average time/residue: 0.1986 time to fit residues: 276.7111 Evaluate side-chains 832 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 832 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 163 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 17 optimal weight: 0.0030 chunk 86 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 overall best weight: 3.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 ASN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A1038 HIS ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 400 ASN B 760 GLN B 879 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 374 GLN C 395 GLN C 461 HIS ** C 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN ** C 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077750 restraints weight = 78840.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080745 restraints weight = 47496.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082856 restraints weight = 31763.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084345 restraints weight = 22836.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085465 restraints weight = 17417.364| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25106 Z= 0.215 Angle : 0.724 8.838 34022 Z= 0.386 Chirality : 0.046 0.202 3789 Planarity : 0.006 0.108 4530 Dihedral : 6.316 119.547 3573 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.52 (0.14), residues: 3210 helix: 0.65 (0.12), residues: 1638 sheet: -0.59 (0.30), residues: 288 loop : -1.58 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 178 TYR 0.035 0.002 TYR C 93 PHE 0.035 0.002 PHE C 959 TRP 0.037 0.003 TRP B 516 HIS 0.008 0.002 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00446 (25106) covalent geometry : angle 0.72418 (34022) hydrogen bonds : bond 0.04348 ( 1267) hydrogen bonds : angle 4.84453 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5453.64 seconds wall clock time: 94 minutes 29.58 seconds (5669.58 seconds total)