Starting phenix.real_space_refine on Fri Mar 6 03:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.map" model { file = "/net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo2_33979/03_2026/7yo2_33979.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 184 5.16 5 C 18096 2.51 5 N 4564 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27884 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6971 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 850} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 6971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6971 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 850} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 6971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6971 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 850} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 5} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 6971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6971 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 850} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 5} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 6.38, per 1000 atoms: 0.23 Number of scatterers: 27884 At special positions: 0 Unit cell: (151.392, 155.376, 152.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 184 16.00 O 5040 8.00 N 4564 7.00 C 18096 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 20 sheets defined 55.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.515A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 109 through 136 removed outlier: 3.523A pdb=" N ASN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.574A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.547A pdb=" N LEU A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.834A pdb=" N GLU A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.745A pdb=" N ILE A 472 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.061A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.671A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.854A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.520A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 4.255A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.814A pdb=" N SER A 922 " --> pdb=" O SER A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 943 removed outlier: 4.415A pdb=" N LEU A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.673A pdb=" N GLU A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 987 through 992 removed outlier: 4.088A pdb=" N ASP A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.700A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.824A pdb=" N MET B 104 " --> pdb=" O TRP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 135 Processing helix chain 'B' and resid 147 through 171 removed outlier: 3.763A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 205 through 214 removed outlier: 4.358A pdb=" N PHE B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 209 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 224 removed outlier: 4.158A pdb=" N GLU B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.708A pdb=" N ILE B 472 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.523A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.711A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.954A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 747 through 751 removed outlier: 3.567A pdb=" N LEU B 751 " --> pdb=" O TYR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 766 through 771 Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.524A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.726A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.989A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 930 removed outlier: 3.724A pdb=" N SER B 922 " --> pdb=" O SER B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 942 removed outlier: 4.380A pdb=" N LEU B 934 " --> pdb=" O ASN B 930 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 removed outlier: 3.632A pdb=" N GLU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 971 removed outlier: 3.510A pdb=" N ASN B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 992 removed outlier: 3.825A pdb=" N ASP B 992 " --> pdb=" O ALA B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.532A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.766A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 109 through 135 removed outlier: 3.643A pdb=" N ARG C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 171 removed outlier: 3.582A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.505A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.885A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 removed outlier: 4.237A pdb=" N GLU C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.721A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.763A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 606 Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.997A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 759 through 767 removed outlier: 3.797A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.539A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.685A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 892 Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 918 through 930 removed outlier: 3.746A pdb=" N SER C 922 " --> pdb=" O SER C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 942 removed outlier: 4.367A pdb=" N LEU C 934 " --> pdb=" O ASN C 930 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 removed outlier: 3.597A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 970 Processing helix chain 'C' and resid 971 through 973 No H-bonds generated for 'chain 'C' and resid 971 through 973' Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.986A pdb=" N ASP C 992 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.792A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.745A pdb=" N MET D 104 " --> pdb=" O TRP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 135 removed outlier: 3.585A pdb=" N ARG D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 171 removed outlier: 3.978A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 180 through 199 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 205 through 214 removed outlier: 4.534A pdb=" N PHE D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 209 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 removed outlier: 4.283A pdb=" N GLU D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.523A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.554A pdb=" N ILE D 472 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.676A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.623A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.862A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 771 removed outlier: 3.912A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.528A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.905A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 4.048A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 918 through 930 removed outlier: 3.739A pdb=" N SER D 922 " --> pdb=" O SER D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 942 removed outlier: 4.382A pdb=" N LEU D 934 " --> pdb=" O ASN D 930 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 939 " --> pdb=" O THR D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 removed outlier: 3.504A pdb=" N GLU D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 973 No H-bonds generated for 'chain 'D' and resid 971 through 973' Processing helix chain 'D' and resid 987 through 992 removed outlier: 4.065A pdb=" N ASP D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1007 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 402 removed outlier: 4.822A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.368A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.438A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.153A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 976 through 981 removed outlier: 4.012A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 402 removed outlier: 4.737A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.259A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.320A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.238A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.927A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.724A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.211A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.565A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.165A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.845A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.912A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.296A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.341A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.302A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 981 removed outlier: 4.007A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8804 1.34 - 1.46: 6782 1.46 - 1.58: 12666 1.58 - 1.70: 0 1.70 - 1.81: 276 Bond restraints: 28528 Sorted by residual: bond pdb=" C VAL B 319 " pdb=" N PRO B 320 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" C VAL D 319 " pdb=" N PRO D 320 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 bond pdb=" C VAL C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.30e+00 bond pdb=" C VAL A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" CG LEU D 281 " pdb=" CD1 LEU D 281 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 ... (remaining 28523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 38133 1.62 - 3.24: 477 3.24 - 4.86: 86 4.86 - 6.48: 27 6.48 - 8.10: 5 Bond angle restraints: 38728 Sorted by residual: angle pdb=" CG ARG A 210 " pdb=" CD ARG A 210 " pdb=" NE ARG A 210 " ideal model delta sigma weight residual 112.00 103.90 8.10 2.20e+00 2.07e-01 1.36e+01 angle pdb=" C TYR B 163 " pdb=" N PHE B 164 " pdb=" CA PHE B 164 " ideal model delta sigma weight residual 121.14 114.90 6.24 1.75e+00 3.27e-01 1.27e+01 angle pdb=" N ILE C 105 " pdb=" CA ILE C 105 " pdb=" C ILE C 105 " ideal model delta sigma weight residual 112.96 110.03 2.93 1.00e+00 1.00e+00 8.57e+00 angle pdb=" N VAL B 288 " pdb=" CA VAL B 288 " pdb=" C VAL B 288 " ideal model delta sigma weight residual 110.74 108.28 2.46 9.10e-01 1.21e+00 7.28e+00 angle pdb=" C TYR C 163 " pdb=" N PHE C 164 " pdb=" CA PHE C 164 " ideal model delta sigma weight residual 120.68 116.18 4.50 1.70e+00 3.46e-01 6.99e+00 ... (remaining 38723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15251 17.99 - 35.97: 1312 35.97 - 53.96: 195 53.96 - 71.95: 41 71.95 - 89.93: 25 Dihedral angle restraints: 16824 sinusoidal: 6528 harmonic: 10296 Sorted by residual: dihedral pdb=" CA GLU C 324 " pdb=" C GLU C 324 " pdb=" N LEU C 325 " pdb=" CA LEU C 325 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG B 213 " pdb=" C ARG B 213 " pdb=" N LEU B 214 " pdb=" CA LEU B 214 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ARG A 213 " pdb=" C ARG A 213 " pdb=" N LEU A 214 " pdb=" CA LEU A 214 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 16821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3356 0.041 - 0.082: 781 0.082 - 0.123: 270 0.123 - 0.164: 37 0.164 - 0.205: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CB VAL A 319 " pdb=" CA VAL A 319 " pdb=" CG1 VAL A 319 " pdb=" CG2 VAL A 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU A 26 " pdb=" CB LEU A 26 " pdb=" CD1 LEU A 26 " pdb=" CD2 LEU A 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CB VAL A 941 " pdb=" CA VAL A 941 " pdb=" CG1 VAL A 941 " pdb=" CG2 VAL A 941 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 4445 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 898 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO C 899 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 191 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 192 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 965 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO D 966 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 966 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 966 " -0.021 5.00e-02 4.00e+02 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 459 2.70 - 3.25: 27957 3.25 - 3.80: 43603 3.80 - 4.35: 58665 4.35 - 4.90: 97553 Nonbonded interactions: 228237 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.148 3.040 nonbonded pdb=" O ARG D 938 " pdb=" OG1 THR D 942 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 284 " pdb=" OH TYR C 290 " model vdw 2.197 3.040 nonbonded pdb=" O ARG C 938 " pdb=" OG1 THR C 942 " model vdw 2.226 3.040 ... (remaining 228232 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.070 Find NCS groups from input model: 0.450 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28528 Z= 0.113 Angle : 0.498 8.100 38728 Z= 0.268 Chirality : 0.040 0.205 4448 Planarity : 0.004 0.052 4860 Dihedral : 13.872 89.934 10152 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3480 helix: 1.02 (0.13), residues: 1616 sheet: -0.25 (0.24), residues: 452 loop : 0.18 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 210 TYR 0.020 0.001 TYR D1015 PHE 0.020 0.001 PHE C 164 TRP 0.012 0.001 TRP B 767 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00241 (28528) covalent geometry : angle 0.49841 (38728) hydrogen bonds : bond 0.15146 ( 1317) hydrogen bonds : angle 5.78470 ( 3600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.6695 (tt0) cc_final: 0.6421 (tt0) REVERT: A 506 MET cc_start: 0.7977 (ttm) cc_final: 0.7656 (mtp) REVERT: A 535 GLU cc_start: 0.7083 (mp0) cc_final: 0.6714 (mp0) REVERT: A 702 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7898 (mmtm) REVERT: A 950 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 1022 LEU cc_start: 0.7023 (mt) cc_final: 0.6808 (mp) REVERT: B 264 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 385 LEU cc_start: 0.8051 (mm) cc_final: 0.7838 (mp) REVERT: B 816 GLN cc_start: 0.7980 (tt0) cc_final: 0.7694 (tt0) REVERT: C 133 ASP cc_start: 0.7607 (m-30) cc_final: 0.7362 (m-30) REVERT: C 188 PHE cc_start: 0.8110 (m-80) cc_final: 0.7632 (m-80) REVERT: C 605 VAL cc_start: 0.8674 (p) cc_final: 0.8425 (t) REVERT: D 94 MET cc_start: 0.2895 (mtt) cc_final: 0.1698 (mpp) REVERT: D 110 LEU cc_start: 0.5742 (mm) cc_final: 0.5228 (tp) REVERT: D 188 PHE cc_start: 0.7789 (m-80) cc_final: 0.7299 (m-80) REVERT: D 206 LEU cc_start: 0.8671 (mm) cc_final: 0.8286 (mt) REVERT: D 207 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7823 (ttp80) REVERT: D 442 MET cc_start: 0.8736 (tpt) cc_final: 0.8328 (mmm) REVERT: D 565 MET cc_start: 0.8840 (ttp) cc_final: 0.8509 (ttt) REVERT: D 969 LEU cc_start: 0.9300 (mt) cc_final: 0.9067 (mt) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.1722 time to fit residues: 108.0787 Evaluate side-chains 295 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 258 ASN A 365 HIS A 465 ASN A 582 ASN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN A 893 GLN B 884 ASN D 465 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102546 restraints weight = 38207.376| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.04 r_work: 0.2854 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28528 Z= 0.157 Angle : 0.522 7.931 38728 Z= 0.275 Chirality : 0.042 0.225 4448 Planarity : 0.004 0.048 4860 Dihedral : 4.139 19.849 3756 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.69 % Allowed : 6.08 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3480 helix: 1.03 (0.13), residues: 1632 sheet: -0.22 (0.24), residues: 456 loop : 0.21 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 790 TYR 0.018 0.001 TYR D1015 PHE 0.030 0.002 PHE B 164 TRP 0.013 0.001 TRP B 767 HIS 0.006 0.001 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00372 (28528) covalent geometry : angle 0.52240 (38728) hydrogen bonds : bond 0.04298 ( 1317) hydrogen bonds : angle 4.92786 ( 3600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 535 GLU cc_start: 0.7887 (mp0) cc_final: 0.7248 (mm-30) REVERT: A 702 LYS cc_start: 0.8397 (mmtp) cc_final: 0.8147 (mmtm) REVERT: B 104 MET cc_start: 0.5832 (ttt) cc_final: 0.5619 (mmm) REVERT: B 264 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 309 LEU cc_start: 0.8125 (mm) cc_final: 0.7740 (mt) REVERT: C 133 ASP cc_start: 0.8047 (m-30) cc_final: 0.7735 (m-30) REVERT: C 506 MET cc_start: 0.8645 (ttm) cc_final: 0.8418 (mtp) REVERT: C 605 VAL cc_start: 0.8498 (p) cc_final: 0.8188 (t) REVERT: C 967 GLN cc_start: 0.8121 (tp40) cc_final: 0.7587 (pt0) REVERT: D 94 MET cc_start: 0.2882 (mtt) cc_final: 0.1589 (mpp) REVERT: D 188 PHE cc_start: 0.8063 (m-80) cc_final: 0.7519 (m-80) REVERT: D 206 LEU cc_start: 0.8807 (mm) cc_final: 0.8433 (mt) REVERT: D 207 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7919 (mtp180) REVERT: D 442 MET cc_start: 0.9352 (tpt) cc_final: 0.9108 (mmm) REVERT: D 565 MET cc_start: 0.9004 (ttp) cc_final: 0.8731 (ttt) REVERT: D 969 LEU cc_start: 0.9367 (mt) cc_final: 0.9119 (mt) outliers start: 21 outliers final: 15 residues processed: 326 average time/residue: 0.1837 time to fit residues: 96.4552 Evaluate side-chains 301 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 328 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 304 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 329 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 341 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.103379 restraints weight = 38415.294| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.05 r_work: 0.2884 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28528 Z= 0.102 Angle : 0.462 8.315 38728 Z= 0.242 Chirality : 0.040 0.153 4448 Planarity : 0.003 0.050 4860 Dihedral : 3.959 19.068 3756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 7.81 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3480 helix: 1.16 (0.13), residues: 1636 sheet: -0.06 (0.25), residues: 440 loop : 0.15 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 167 TYR 0.015 0.001 TYR B 528 PHE 0.025 0.001 PHE B 164 TRP 0.013 0.001 TRP A 22 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00224 (28528) covalent geometry : angle 0.46166 (38728) hydrogen bonds : bond 0.03663 ( 1317) hydrogen bonds : angle 4.73445 ( 3600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7816 (tt0) cc_final: 0.7595 (tt0) REVERT: A 535 GLU cc_start: 0.7814 (mp0) cc_final: 0.7170 (mm-30) REVERT: A 702 LYS cc_start: 0.8419 (mmtp) cc_final: 0.8162 (mmtm) REVERT: B 94 MET cc_start: 0.4040 (mtp) cc_final: 0.3627 (mtt) REVERT: B 264 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 265 ASN cc_start: 0.8467 (t0) cc_final: 0.7786 (t0) REVERT: C 133 ASP cc_start: 0.8035 (m-30) cc_final: 0.7663 (m-30) REVERT: C 506 MET cc_start: 0.8592 (ttm) cc_final: 0.8333 (mtp) REVERT: C 605 VAL cc_start: 0.8471 (p) cc_final: 0.8130 (t) REVERT: C 967 GLN cc_start: 0.8135 (tp40) cc_final: 0.7625 (pt0) REVERT: D 94 MET cc_start: 0.2878 (mtt) cc_final: 0.1585 (mpp) REVERT: D 188 PHE cc_start: 0.8019 (m-80) cc_final: 0.7516 (m-80) REVERT: D 206 LEU cc_start: 0.8752 (mm) cc_final: 0.8361 (mt) REVERT: D 207 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7876 (mtp85) REVERT: D 442 MET cc_start: 0.9316 (tpt) cc_final: 0.9106 (mmm) REVERT: D 565 MET cc_start: 0.8972 (ttp) cc_final: 0.8744 (ttt) outliers start: 22 outliers final: 13 residues processed: 325 average time/residue: 0.1807 time to fit residues: 93.9032 Evaluate side-chains 296 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 283 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 40 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 275 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 329 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105324 restraints weight = 37906.576| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.02 r_work: 0.2885 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28528 Z= 0.102 Angle : 0.454 9.764 38728 Z= 0.238 Chirality : 0.040 0.152 4448 Planarity : 0.003 0.049 4860 Dihedral : 3.851 18.651 3756 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.11 % Allowed : 8.92 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3480 helix: 1.25 (0.13), residues: 1644 sheet: -0.15 (0.25), residues: 456 loop : 0.26 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 960 TYR 0.014 0.001 TYR B 528 PHE 0.025 0.001 PHE B 187 TRP 0.009 0.001 TRP B 178 HIS 0.004 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00232 (28528) covalent geometry : angle 0.45384 (38728) hydrogen bonds : bond 0.03399 ( 1317) hydrogen bonds : angle 4.59518 ( 3600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7552 (m-80) cc_final: 0.7270 (t80) REVERT: A 535 GLU cc_start: 0.7815 (mp0) cc_final: 0.7113 (mm-30) REVERT: A 702 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8155 (mmtm) REVERT: B 264 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 265 ASN cc_start: 0.8478 (t0) cc_final: 0.7786 (t0) REVERT: B 323 ILE cc_start: 0.8171 (mm) cc_final: 0.7861 (mt) REVERT: C 133 ASP cc_start: 0.8050 (m-30) cc_final: 0.7655 (m-30) REVERT: C 506 MET cc_start: 0.8651 (ttm) cc_final: 0.8402 (mtp) REVERT: C 605 VAL cc_start: 0.8483 (p) cc_final: 0.8139 (t) REVERT: C 967 GLN cc_start: 0.8134 (tp40) cc_final: 0.7619 (pt0) REVERT: D 94 MET cc_start: 0.2877 (mtt) cc_final: 0.1581 (mpp) REVERT: D 188 PHE cc_start: 0.8030 (m-80) cc_final: 0.7539 (m-80) REVERT: D 206 LEU cc_start: 0.8700 (mm) cc_final: 0.8408 (mt) REVERT: D 207 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7847 (mtp85) REVERT: D 442 MET cc_start: 0.9308 (tpt) cc_final: 0.9082 (mmm) outliers start: 34 outliers final: 26 residues processed: 329 average time/residue: 0.1798 time to fit residues: 95.4667 Evaluate side-chains 311 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 120 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN A1021 HIS C 534 ASN C 747 HIS D 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099549 restraints weight = 38403.120| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.00 r_work: 0.2818 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28528 Z= 0.205 Angle : 0.543 8.127 38728 Z= 0.283 Chirality : 0.043 0.173 4448 Planarity : 0.004 0.050 4860 Dihedral : 4.212 20.699 3756 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.24 % Allowed : 10.20 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3480 helix: 0.96 (0.13), residues: 1664 sheet: -0.09 (0.25), residues: 444 loop : 0.10 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.014 0.002 TYR B 130 PHE 0.025 0.002 PHE B 187 TRP 0.012 0.001 TRP A 22 HIS 0.008 0.001 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00499 (28528) covalent geometry : angle 0.54317 (38728) hydrogen bonds : bond 0.04294 ( 1317) hydrogen bonds : angle 4.81891 ( 3600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.6715 (tpp) cc_final: 0.6171 (ttp) REVERT: A 535 GLU cc_start: 0.7830 (mp0) cc_final: 0.7018 (mm-30) REVERT: A 702 LYS cc_start: 0.8413 (mmtp) cc_final: 0.8158 (mmtm) REVERT: C 133 ASP cc_start: 0.8085 (m-30) cc_final: 0.7719 (m-30) REVERT: C 605 VAL cc_start: 0.8556 (p) cc_final: 0.8217 (t) REVERT: D 94 MET cc_start: 0.2728 (mtt) cc_final: 0.1441 (mpp) REVERT: D 188 PHE cc_start: 0.8126 (m-80) cc_final: 0.7632 (m-80) REVERT: D 200 ASN cc_start: 0.6113 (t0) cc_final: 0.5832 (t0) REVERT: D 206 LEU cc_start: 0.8863 (mm) cc_final: 0.8573 (mt) REVERT: D 207 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7968 (mtp85) REVERT: D 442 MET cc_start: 0.9380 (tpt) cc_final: 0.9133 (mmm) REVERT: D 565 MET cc_start: 0.9010 (ttp) cc_final: 0.8728 (ttt) REVERT: D 830 MET cc_start: 0.9157 (mtt) cc_final: 0.8937 (mtt) outliers start: 38 outliers final: 31 residues processed: 325 average time/residue: 0.1757 time to fit residues: 92.7982 Evaluate side-chains 310 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 238 optimal weight: 0.0030 chunk 267 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN D 350 HIS D 409 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101229 restraints weight = 38325.593| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.03 r_work: 0.2816 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28528 Z= 0.151 Angle : 0.499 8.587 38728 Z= 0.260 Chirality : 0.041 0.153 4448 Planarity : 0.004 0.050 4860 Dihedral : 4.139 20.632 3756 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.50 % Allowed : 10.65 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3480 helix: 1.11 (0.13), residues: 1628 sheet: -0.11 (0.25), residues: 444 loop : 0.17 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 455 TYR 0.015 0.001 TYR B 130 PHE 0.022 0.001 PHE B 187 TRP 0.010 0.001 TRP A 22 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00363 (28528) covalent geometry : angle 0.49881 (38728) hydrogen bonds : bond 0.03868 ( 1317) hydrogen bonds : angle 4.74816 ( 3600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.6928 (tpp) cc_final: 0.6383 (ttp) REVERT: A 535 GLU cc_start: 0.7846 (mp0) cc_final: 0.6956 (mm-30) REVERT: A 702 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8122 (mmtm) REVERT: A 960 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7565 (ttp-110) REVERT: B 323 ILE cc_start: 0.8226 (mm) cc_final: 0.7958 (mt) REVERT: C 133 ASP cc_start: 0.8075 (m-30) cc_final: 0.7700 (m-30) REVERT: C 366 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7796 (tttp) REVERT: C 513 MET cc_start: 0.7052 (mmm) cc_final: 0.6603 (mmt) REVERT: D 94 MET cc_start: 0.2777 (mtt) cc_final: 0.1518 (mpp) REVERT: D 188 PHE cc_start: 0.8095 (m-80) cc_final: 0.7600 (m-80) REVERT: D 206 LEU cc_start: 0.8784 (mm) cc_final: 0.8583 (mt) REVERT: D 207 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7854 (mtp180) REVERT: D 442 MET cc_start: 0.9362 (tpt) cc_final: 0.9139 (mmm) REVERT: D 565 MET cc_start: 0.9044 (ttp) cc_final: 0.8756 (ttt) REVERT: D 830 MET cc_start: 0.9096 (mtt) cc_final: 0.8887 (mtt) outliers start: 46 outliers final: 37 residues processed: 326 average time/residue: 0.1797 time to fit residues: 94.9146 Evaluate side-chains 315 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 162 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 301 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 329 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 0.0170 chunk 292 optimal weight: 0.9980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101934 restraints weight = 38376.175| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.02 r_work: 0.2876 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28528 Z= 0.096 Angle : 0.456 9.386 38728 Z= 0.237 Chirality : 0.039 0.152 4448 Planarity : 0.003 0.049 4860 Dihedral : 3.860 20.039 3756 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.21 % Allowed : 11.21 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3480 helix: 1.30 (0.13), residues: 1656 sheet: -0.12 (0.25), residues: 444 loop : 0.21 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.015 0.001 TYR B 528 PHE 0.026 0.001 PHE B 168 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00213 (28528) covalent geometry : angle 0.45568 (38728) hydrogen bonds : bond 0.03242 ( 1317) hydrogen bonds : angle 4.54984 ( 3600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.6988 (tpp) cc_final: 0.6407 (ttp) REVERT: A 318 TYR cc_start: 0.7765 (m-80) cc_final: 0.7443 (t80) REVERT: A 535 GLU cc_start: 0.7674 (mp0) cc_final: 0.6963 (mm-30) REVERT: A 702 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8134 (mmtm) REVERT: A 960 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7551 (ttp-110) REVERT: A 980 LEU cc_start: 0.8418 (pp) cc_final: 0.7492 (mt) REVERT: B 187 PHE cc_start: 0.7589 (m-80) cc_final: 0.7289 (m-80) REVERT: B 323 ILE cc_start: 0.8158 (mm) cc_final: 0.7892 (mt) REVERT: C 133 ASP cc_start: 0.8000 (m-30) cc_final: 0.7604 (m-30) REVERT: C 366 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7780 (tttp) REVERT: C 605 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8276 (t) REVERT: D 94 MET cc_start: 0.2689 (mtt) cc_final: 0.1424 (mpp) REVERT: D 188 PHE cc_start: 0.8060 (m-80) cc_final: 0.7600 (m-80) REVERT: D 206 LEU cc_start: 0.8653 (mm) cc_final: 0.8389 (mt) REVERT: D 207 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7836 (mtp85) outliers start: 37 outliers final: 30 residues processed: 327 average time/residue: 0.1792 time to fit residues: 95.2815 Evaluate side-chains 313 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 315 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 232 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102731 restraints weight = 38163.916| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.05 r_work: 0.2853 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28528 Z= 0.143 Angle : 0.494 9.930 38728 Z= 0.255 Chirality : 0.041 0.167 4448 Planarity : 0.004 0.049 4860 Dihedral : 3.959 19.588 3756 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.41 % Allowed : 11.24 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3480 helix: 1.26 (0.13), residues: 1652 sheet: -0.11 (0.25), residues: 444 loop : 0.17 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 368 TYR 0.015 0.001 TYR B 318 PHE 0.029 0.001 PHE B 168 TRP 0.017 0.001 TRP B 178 HIS 0.005 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00344 (28528) covalent geometry : angle 0.49383 (38728) hydrogen bonds : bond 0.03648 ( 1317) hydrogen bonds : angle 4.62137 ( 3600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.7052 (tpp) cc_final: 0.6490 (ttp) REVERT: A 318 TYR cc_start: 0.7827 (m-80) cc_final: 0.7477 (t80) REVERT: A 535 GLU cc_start: 0.7764 (mp0) cc_final: 0.7009 (mm-30) REVERT: A 702 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8166 (mmtm) REVERT: A 960 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7550 (ttp-110) REVERT: A 980 LEU cc_start: 0.8385 (pp) cc_final: 0.7540 (mt) REVERT: B 122 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5563 (mp) REVERT: B 323 ILE cc_start: 0.8193 (mm) cc_final: 0.7922 (mt) REVERT: C 133 ASP cc_start: 0.8085 (m-30) cc_final: 0.7687 (m-30) REVERT: C 366 LYS cc_start: 0.8005 (mmmm) cc_final: 0.7782 (tttp) REVERT: C 605 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8297 (t) REVERT: D 94 MET cc_start: 0.2787 (mtt) cc_final: 0.1517 (mpp) REVERT: D 188 PHE cc_start: 0.8129 (m-80) cc_final: 0.7695 (m-80) REVERT: D 206 LEU cc_start: 0.8774 (mm) cc_final: 0.8521 (mt) REVERT: D 207 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7886 (mtp85) REVERT: D 565 MET cc_start: 0.9070 (ttp) cc_final: 0.8782 (ttt) outliers start: 43 outliers final: 35 residues processed: 320 average time/residue: 0.1744 time to fit residues: 90.9106 Evaluate side-chains 317 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 782 THR Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 117 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 314 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN C 585 ASN C 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101854 restraints weight = 38464.261| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.08 r_work: 0.2863 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28528 Z= 0.095 Angle : 0.459 11.714 38728 Z= 0.237 Chirality : 0.040 0.161 4448 Planarity : 0.003 0.054 4860 Dihedral : 3.784 19.933 3756 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.27 % Allowed : 11.50 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3480 helix: 1.32 (0.13), residues: 1680 sheet: -0.11 (0.25), residues: 444 loop : 0.13 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 368 TYR 0.015 0.001 TYR B 528 PHE 0.035 0.001 PHE B 168 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00212 (28528) covalent geometry : angle 0.45914 (38728) hydrogen bonds : bond 0.03152 ( 1317) hydrogen bonds : angle 4.48667 ( 3600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.7035 (tpp) cc_final: 0.6490 (ttp) REVERT: A 318 TYR cc_start: 0.7760 (m-80) cc_final: 0.7429 (t80) REVERT: A 535 GLU cc_start: 0.7671 (mp0) cc_final: 0.6955 (mm-30) REVERT: A 960 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7532 (ttp-110) REVERT: A 980 LEU cc_start: 0.8330 (pp) cc_final: 0.7464 (mt) REVERT: B 122 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5657 (mp) REVERT: B 231 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7204 (t0) REVERT: B 264 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 323 ILE cc_start: 0.8046 (mm) cc_final: 0.7759 (mt) REVERT: C 30 MET cc_start: 0.6085 (mtt) cc_final: 0.5730 (ttp) REVERT: C 133 ASP cc_start: 0.8059 (m-30) cc_final: 0.7679 (m-30) REVERT: C 366 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7769 (tttp) REVERT: C 605 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8273 (t) REVERT: D 94 MET cc_start: 0.2793 (mtt) cc_final: 0.1502 (mpp) REVERT: D 188 PHE cc_start: 0.8063 (m-80) cc_final: 0.7668 (m-80) REVERT: D 206 LEU cc_start: 0.8606 (mm) cc_final: 0.8345 (mt) REVERT: D 207 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7908 (mtp85) REVERT: D 323 ILE cc_start: 0.7438 (mm) cc_final: 0.7229 (mm) REVERT: D 565 MET cc_start: 0.9059 (ttp) cc_final: 0.8779 (ttt) outliers start: 39 outliers final: 30 residues processed: 328 average time/residue: 0.1639 time to fit residues: 87.8147 Evaluate side-chains 317 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 585 ASN Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 179 optimal weight: 5.9990 chunk 285 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 150 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 94 optimal weight: 0.0670 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN C 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103266 restraints weight = 38055.643| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.09 r_work: 0.2864 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 28528 Z= 0.126 Angle : 0.595 59.162 38728 Z= 0.335 Chirality : 0.041 0.617 4448 Planarity : 0.003 0.051 4860 Dihedral : 3.808 26.613 3756 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.02 % Rotamer: Outliers : 1.14 % Allowed : 11.70 % Favored : 87.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3480 helix: 1.32 (0.13), residues: 1680 sheet: -0.11 (0.25), residues: 444 loop : 0.12 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.014 0.001 TYR B 528 PHE 0.030 0.001 PHE B 168 TRP 0.016 0.001 TRP B 178 HIS 0.003 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00277 (28528) covalent geometry : angle 0.59544 (38728) hydrogen bonds : bond 0.03177 ( 1317) hydrogen bonds : angle 4.48569 ( 3600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.7017 (tpp) cc_final: 0.6468 (ttp) REVERT: A 318 TYR cc_start: 0.7765 (m-80) cc_final: 0.7431 (t80) REVERT: A 535 GLU cc_start: 0.7658 (mp0) cc_final: 0.6934 (mm-30) REVERT: A 960 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: A 980 LEU cc_start: 0.8311 (pp) cc_final: 0.7458 (mt) REVERT: B 122 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5760 (mp) REVERT: B 264 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 323 ILE cc_start: 0.8042 (mm) cc_final: 0.7746 (mt) REVERT: C 30 MET cc_start: 0.6110 (mtt) cc_final: 0.5753 (ttp) REVERT: C 133 ASP cc_start: 0.8060 (m-30) cc_final: 0.7681 (m-30) REVERT: C 366 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7771 (tttp) REVERT: C 605 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8270 (t) REVERT: D 94 MET cc_start: 0.2801 (mtt) cc_final: 0.1505 (mpp) REVERT: D 188 PHE cc_start: 0.8060 (m-80) cc_final: 0.7584 (m-80) REVERT: D 206 LEU cc_start: 0.8605 (mm) cc_final: 0.8343 (mt) REVERT: D 207 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7903 (mtp85) REVERT: D 323 ILE cc_start: 0.7434 (mm) cc_final: 0.7226 (mm) REVERT: D 565 MET cc_start: 0.9054 (ttp) cc_final: 0.8771 (ttt) outliers start: 35 outliers final: 31 residues processed: 310 average time/residue: 0.1738 time to fit residues: 88.0538 Evaluate side-chains 315 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 884 ASN Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 953 ILE Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 317 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN C 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103896 restraints weight = 37999.900| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.05 r_work: 0.2864 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28528 Z= 0.107 Angle : 0.472 12.769 38728 Z= 0.243 Chirality : 0.040 0.262 4448 Planarity : 0.003 0.060 4860 Dihedral : 3.781 19.231 3756 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 11.70 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.14), residues: 3480 helix: 1.34 (0.13), residues: 1680 sheet: -0.10 (0.25), residues: 444 loop : 0.14 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.014 0.001 TYR B 130 PHE 0.036 0.001 PHE B 187 TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00248 (28528) covalent geometry : angle 0.47192 (38728) hydrogen bonds : bond 0.03264 ( 1317) hydrogen bonds : angle 4.47654 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.30 seconds wall clock time: 119 minutes 33.74 seconds (7173.74 seconds total)