Starting phenix.real_space_refine on Sun Jul 5 02:56:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu7_29454/07_2026/8fu7_29454.map" } resolution = 3.21 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= 0.002 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 108 5.16 5 C 16071 2.51 5 N 4137 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B GLU 449": not complete - not flipped Time to flip 145 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25020 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 38} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 38} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 38} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 5.70, per 1000 atoms: 0.23 Number of scatterers: 25020 At special positions: 0 Unit cell: (141.474, 135.649, 172.265, 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 108 16.00 O 4704 8.00 N 4137 7.00 C 16071 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: 2.28 Conformation dependent library (CDL) restraints added in 822.9 milliseconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5874 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 42 sheets defined 25.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.952A pdb=" N GLY A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.896A pdb=" N ALA A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.794A pdb=" N ASP A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 850 through 869 Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.186A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 925 Processing helix chain 'A' and resid 929 through 949 removed outlier: 3.924A pdb=" N VAL A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 966 Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.402A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.976A pdb=" N GLY B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.515A pdb=" N TRP B 337 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.881A pdb=" N ALA B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.588A pdb=" N VAL B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.772A pdb=" N ASP B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 850 through 869 Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 881 through 892 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.216A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 925 Processing helix chain 'B' and resid 929 through 949 removed outlier: 3.917A pdb=" N VAL B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 960 through 966 Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.446A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.967A pdb=" N GLY C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.574A pdb=" N TRP C 337 " --> pdb=" O VAL C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 390 through 395 removed outlier: 3.902A pdb=" N ALA C 395 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.593A pdb=" N VAL C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 767 removed outlier: 3.758A pdb=" N ASP C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 810 Processing helix chain 'C' and resid 850 through 869 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 903 removed outlier: 4.174A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 925 Processing helix chain 'C' and resid 929 through 949 removed outlier: 3.905A pdb=" N VAL C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 966 Processing helix chain 'C' and resid 969 through 1017 removed outlier: 4.396A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1130 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.680A pdb=" N ASN A 61 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A 253 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 192 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP A 219 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 194 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.388A pdb=" N GLY C 550 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP C 558 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.303A pdb=" N THR A 258 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP A 274 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 260 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 272 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS A 262 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.639A pdb=" N VAL A 130 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE A 159 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 300 removed outlier: 6.933A pdb=" N VAL A 579 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 312 removed outlier: 5.763A pdb=" N ASP A 558 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 550 " --> pdb=" O ASP A 558 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 549 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 342 removed outlier: 5.527A pdb=" N ASN A 378 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 500 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.515A pdb=" N CYS A 345 " --> pdb=" O CYS A 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.220A pdb=" N LEU A 436 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.605A pdb=" N ILE A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 688 removed outlier: 6.503A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS B 774 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 687 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 695 through 699 removed outlier: 4.252A pdb=" N PHE A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 712 removed outlier: 6.019A pdb=" N TYR A1051 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS A1032 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.298A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 771 through 774 Processing sheet with id=AB7, first strand: chain 'A' and resid 1104 through 1109 removed outlier: 4.789A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.904A pdb=" N ASN B 61 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR B 253 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 192 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP B 219 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.227A pdb=" N THR B 258 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 274 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 260 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 272 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 262 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.971A pdb=" N GLY B 103 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 300 removed outlier: 6.932A pdb=" N VAL B 579 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 312 removed outlier: 5.843A pdb=" N ASP B 558 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 550 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE B 549 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 338 through 342 removed outlier: 5.529A pdb=" N ASN B 378 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 500 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.578A pdb=" N CYS B 345 " --> pdb=" O CYS B 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 436 through 437 removed outlier: 4.427A pdb=" N LEU B 436 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.606A pdb=" N ILE B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 685 through 688 removed outlier: 6.441A pdb=" N ALA B 685 " --> pdb=" O ILE C 772 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LYS C 774 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN B 687 " --> pdb=" O LYS C 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.725A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.725A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.309A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 4.784A pdb=" N ALA B1071 " --> pdb=" O SER B1107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.971A pdb=" N ASN C 61 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 253 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.231A pdb=" N THR C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 274 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 260 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA C 272 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS C 262 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.000A pdb=" N GLY C 103 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 300 removed outlier: 6.931A pdb=" N VAL C 579 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 338 through 342 removed outlier: 5.521A pdb=" N ASN C 378 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 500 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.537A pdb=" N CYS C 345 " --> pdb=" O CYS C 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 436 through 437 removed outlier: 4.370A pdb=" N LEU C 436 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 638 through 644 removed outlier: 5.022A pdb=" N THR C 680 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C 642 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.042A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.042A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.266A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 4.792A pdb=" N ALA C1071 " --> pdb=" O SER C1107 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2802 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: 7.50 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6255 1.33 - 1.46: 6524 1.46 - 1.58: 12676 1.58 - 1.71: 6 1.71 - 1.84: 138 Bond restraints: 25599 Sorted by residual: bond pdb=" C1 NAG A1211 " pdb=" O1 NAG A1211 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C1 NAG B1211 " pdb=" O1 NAG B1211 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C1 NAG A1210 " pdb=" O1 NAG A1210 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG C1203 " pdb=" O1 NAG C1203 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG A1203 " pdb=" O1 NAG A1203 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 25594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 30471 1.81 - 3.63: 3485 3.63 - 5.44: 533 5.44 - 7.26: 210 7.26 - 9.07: 17 Bond angle restraints: 34716 Sorted by residual: angle pdb=" C LEU C 24 " pdb=" N PRO C 25 " pdb=" CA PRO C 25 " ideal model delta sigma weight residual 119.66 126.55 -6.89 7.20e-01 1.93e+00 9.16e+01 angle pdb=" C LEU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C LEU C 845 " pdb=" N PRO C 846 " pdb=" CA PRO C 846 " ideal model delta sigma weight residual 119.66 125.17 -5.51 7.20e-01 1.93e+00 5.86e+01 angle pdb=" C LEU A 845 " pdb=" N PRO A 846 " pdb=" CA PRO A 846 " ideal model delta sigma weight residual 119.66 125.08 -5.42 7.20e-01 1.93e+00 5.67e+01 ... (remaining 34711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.53: 14440 20.53 - 41.06: 335 41.06 - 61.60: 76 61.60 - 82.13: 28 82.13 - 102.66: 7 Dihedral angle restraints: 14886 sinusoidal: 5751 harmonic: 9135 Sorted by residual: dihedral pdb=" CB GLU B 449 " pdb=" CG GLU B 449 " pdb=" CD GLU B 449 " pdb=" OE1 GLU B 449 " ideal model delta sinusoidal sigma weight residual 0.00 102.66 -102.66 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CA GLN B 490 " pdb=" C GLN B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLN A 490 " pdb=" C GLN A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 14883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3194 0.084 - 0.168: 689 0.168 - 0.252: 130 0.252 - 0.335: 96 0.335 - 0.419: 4 Chirality restraints: 4113 Sorted by residual: chirality pdb=" CA ALA C 877 " pdb=" N ALA C 877 " pdb=" C ALA C 877 " pdb=" CB ALA C 877 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CG LEU A 24 " pdb=" CB LEU A 24 " pdb=" CD1 LEU A 24 " pdb=" CD2 LEU A 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU C 24 " pdb=" CB LEU C 24 " pdb=" CD1 LEU C 24 " pdb=" CD2 LEU C 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4110 not shown) Planarity restraints: 4239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 437 " -0.038 2.00e-02 2.50e+03 2.14e-02 9.12e+00 pdb=" CG TYR B 437 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 437 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 437 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 437 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 437 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 437 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 437 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 437 " -0.032 2.00e-02 2.50e+03 1.81e-02 6.52e+00 pdb=" CG TYR C 437 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR C 437 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 437 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C 437 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR C 437 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 437 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 437 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1204 " -0.025 2.00e-02 2.50e+03 2.05e-02 5.23e+00 pdb=" C7 NAG A1204 " 0.004 2.00e-02 2.50e+03 pdb=" C8 NAG A1204 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG A1204 " 0.032 2.00e-02 2.50e+03 pdb=" O7 NAG A1204 " 0.007 2.00e-02 2.50e+03 ... (remaining 4236 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1164 2.71 - 3.26: 24679 3.26 - 3.80: 39718 3.80 - 4.35: 51846 4.35 - 4.90: 86225 Nonbonded interactions: 203632 Sorted by model distance: nonbonded pdb=" ND2 ASN B 378 " pdb=" OH TYR C 191 " model vdw 2.159 3.120 nonbonded pdb=" OH TYR A 191 " pdb=" ND2 ASN C 378 " model vdw 2.171 3.120 nonbonded pdb=" ND2 ASN A 378 " pdb=" OH TYR B 191 " model vdw 2.175 3.120 nonbonded pdb=" O LEU C 277 " pdb=" OG1 THR C 616 " model vdw 2.338 3.040 nonbonded pdb=" O LEU B 277 " pdb=" OG1 THR B 616 " model vdw 2.352 3.040 ... (remaining 203627 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 8.170 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.000 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.012 0.106 25599 Z= 0.668 Angle : 1.297 9.070 34716 Z= 0.875 Chirality : 0.082 0.419 4113 Planarity : 0.005 0.029 4239 Dihedral : 10.413 102.659 9012 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.18 % Favored : 93.95 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.35 (0.14), residues: 3108 helix: 0.50 (0.18), residues: 663 sheet: 1.05 (0.20), residues: 570 loop : -0.95 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 984 TYR 0.038 0.005 TYR B 437 PHE 0.025 0.003 PHE A 474 TRP 0.024 0.004 TRP C 64 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.01241 / 0.67 (25599) covalent geometry : angle 1.29703 / 0.87 (34716) hydrogen bonds : bond 0.17019 / 11.39 ( 1018) hydrogen bonds : angle 8.13780 / 5.66 ( 2802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 490 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6990 (m-40) cc_final: 0.6763 (t0) REVERT: A 319 LEU cc_start: 0.6677 (mt) cc_final: 0.6217 (tp) REVERT: A 344 ASN cc_start: 0.8066 (m-40) cc_final: 0.7842 (m-40) REVERT: A 360 THR cc_start: 0.6356 (t) cc_final: 0.6142 (p) REVERT: A 378 ASN cc_start: 0.6430 (m-40) cc_final: 0.6059 (m-40) REVERT: A 380 TYR cc_start: 0.6967 (m-80) cc_final: 0.6717 (m-80) REVERT: A 392 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7474 (ppt170) REVERT: A 405 TYR cc_start: 0.7580 (m-80) cc_final: 0.6996 (m-80) REVERT: A 408 LYS cc_start: 0.6716 (tttp) cc_final: 0.6493 (tptp) REVERT: A 497 LEU cc_start: 0.8464 (mt) cc_final: 0.8257 (mp) REVERT: A 498 SER cc_start: 0.8000 (t) cc_final: 0.7576 (p) REVERT: A 625 ASN cc_start: 0.6984 (m-40) cc_final: 0.6473 (p0) REVERT: A 919 GLN cc_start: 0.6964 (mt0) cc_final: 0.6633 (mt0) REVERT: B 121 ASN cc_start: 0.7042 (m-40) cc_final: 0.6783 (t0) REVERT: B 196 SER cc_start: 0.9012 (p) cc_final: 0.8598 (m) REVERT: B 340 LYS cc_start: 0.7411 (tttp) cc_final: 0.7162 (tttt) REVERT: B 344 ASN cc_start: 0.8117 (m-40) cc_final: 0.7903 (m-40) REVERT: B 378 ASN cc_start: 0.6508 (m-40) cc_final: 0.6306 (m-40) REVERT: B 380 TYR cc_start: 0.7171 (m-80) cc_final: 0.6796 (m-80) REVERT: B 393 GLN cc_start: 0.7661 (mt0) cc_final: 0.7335 (tt0) REVERT: B 405 TYR cc_start: 0.7546 (m-80) cc_final: 0.6916 (m-80) REVERT: B 408 LYS cc_start: 0.6680 (tttp) cc_final: 0.6344 (tptp) REVERT: B 498 SER cc_start: 0.7880 (t) cc_final: 0.7485 (p) REVERT: B 625 ASN cc_start: 0.7074 (m-40) cc_final: 0.6510 (p0) REVERT: B 919 GLN cc_start: 0.7179 (mt0) cc_final: 0.6966 (mt0) REVERT: C 28 TYR cc_start: 0.3827 (m-80) cc_final: 0.3565 (m-80) REVERT: C 105 ILE cc_start: 0.7899 (mt) cc_final: 0.7637 (mm) REVERT: C 310 ILE cc_start: 0.7440 (mt) cc_final: 0.7213 (pt) REVERT: C 319 LEU cc_start: 0.6525 (mt) cc_final: 0.6155 (tp) REVERT: C 344 ASN cc_start: 0.8088 (m-40) cc_final: 0.7806 (m-40) REVERT: C 378 ASN cc_start: 0.6396 (m-40) cc_final: 0.5990 (m-40) REVERT: C 392 ARG cc_start: 0.7745 (ptt90) cc_final: 0.7533 (ppt170) REVERT: C 408 LYS cc_start: 0.6845 (tttp) cc_final: 0.6510 (tptp) REVERT: C 498 SER cc_start: 0.8021 (t) cc_final: 0.7612 (p) REVERT: C 888 TYR cc_start: 0.7380 (m-10) cc_final: 0.7004 (m-10) outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.1588 time to fit residues: 119.2693 Evaluate side-chains 274 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS A 994 GLN B 198 HIS B 587 ASN B 701 ASN B 748 ASN B 994 GLN B1058 ASN C 121 ASN C 378 ASN C 587 ASN C 701 ASN C 748 ASN C 897 GLN C1058 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118131 restraints weight = 39428.795| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.24 r_work: 0.3130 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25599 Z= 0.149 Angle : 0.635 8.090 34716 Z= 0.342 Chirality : 0.046 0.233 4113 Planarity : 0.005 0.047 4239 Dihedral : 4.661 22.960 3363 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 1.24 % Allowed : 4.40 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.03 (0.15), residues: 3108 helix: 1.87 (0.21), residues: 666 sheet: 1.25 (0.21), residues: 582 loop : -1.16 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 441 TYR 0.022 0.001 TYR B 161 PHE 0.034 0.002 PHE B 135 TRP 0.009 0.001 TRP A 420 HIS 0.019 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (25599) covalent geometry : angle 0.63534 / 0.34 (34716) hydrogen bonds : bond 0.05286 / 3.50 ( 1018) hydrogen bonds : angle 6.14530 / 4.30 ( 2802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7587 (m-80) cc_final: 0.7180 (m-80) REVERT: A 196 SER cc_start: 0.8731 (p) cc_final: 0.8456 (m) REVERT: A 319 LEU cc_start: 0.6675 (mt) cc_final: 0.6336 (tp) REVERT: A 380 TYR cc_start: 0.7434 (m-80) cc_final: 0.7117 (m-80) REVERT: A 408 LYS cc_start: 0.7174 (tttp) cc_final: 0.6816 (tptp) REVERT: A 941 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: B 121 ASN cc_start: 0.7148 (m-40) cc_final: 0.6917 (t0) REVERT: B 196 SER cc_start: 0.8812 (p) cc_final: 0.8525 (m) REVERT: B 313 PHE cc_start: 0.7062 (m-80) cc_final: 0.6861 (m-10) REVERT: B 319 LEU cc_start: 0.6844 (mm) cc_final: 0.6431 (tp) REVERT: B 380 TYR cc_start: 0.7510 (m-80) cc_final: 0.7155 (m-80) REVERT: B 408 LYS cc_start: 0.7155 (tttp) cc_final: 0.6705 (tptp) REVERT: B 568 ILE cc_start: 0.8307 (mm) cc_final: 0.7974 (pt) REVERT: B 891 ASN cc_start: 0.8659 (t0) cc_final: 0.8385 (t0) REVERT: C 105 ILE cc_start: 0.8039 (mt) cc_final: 0.7779 (mm) REVERT: C 125 ASN cc_start: 0.6891 (m-40) cc_final: 0.6626 (m-40) REVERT: C 181 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7479 (mtm-85) REVERT: C 196 SER cc_start: 0.8804 (p) cc_final: 0.8530 (m) REVERT: C 319 LEU cc_start: 0.6704 (mt) cc_final: 0.6445 (tp) REVERT: C 408 LYS cc_start: 0.7232 (tttp) cc_final: 0.6762 (tptp) REVERT: C 448 PHE cc_start: 0.6830 (m-80) cc_final: 0.6308 (m-80) outliers start: 34 outliers final: 19 residues processed: 363 average time/residue: 0.1487 time to fit residues: 87.6050 Evaluate side-chains 275 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 393 GLN A 600 ASN A1032 HIS B 315 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 600 ASN B 639 HIS B 701 ASN ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1032 HIS C 230 GLN C 315 ASN C 587 ASN C 600 ASN C 701 ASN C1032 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114399 restraints weight = 39306.374| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.23 r_work: 0.3065 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25599 Z= 0.211 Angle : 0.650 7.859 34716 Z= 0.344 Chirality : 0.047 0.248 4113 Planarity : 0.005 0.052 4239 Dihedral : 4.854 25.150 3363 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.26 % Allowed : 6.73 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.33 (0.15), residues: 3108 helix: 1.82 (0.21), residues: 663 sheet: 0.89 (0.21), residues: 597 loop : -1.47 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 228 TYR 0.029 0.002 TYR A 161 PHE 0.027 0.002 PHE A 474 TRP 0.017 0.001 TRP B1086 HIS 0.016 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (25599) covalent geometry : angle 0.64989 / 0.34 (34716) hydrogen bonds : bond 0.05410 / 3.58 ( 1018) hydrogen bonds : angle 5.87312 / 4.11 ( 2802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 274 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7702 (m-80) cc_final: 0.7387 (m-80) REVERT: A 168 MET cc_start: 0.5188 (tmm) cc_final: 0.4859 (tpp) REVERT: A 380 TYR cc_start: 0.7559 (m-80) cc_final: 0.7098 (m-80) REVERT: A 408 LYS cc_start: 0.7235 (tttp) cc_final: 0.6818 (tptp) REVERT: A 576 PHE cc_start: 0.7872 (p90) cc_final: 0.7275 (p90) REVERT: B 168 MET cc_start: 0.5046 (tmm) cc_final: 0.4670 (tpp) REVERT: B 313 PHE cc_start: 0.6980 (m-80) cc_final: 0.6741 (m-10) REVERT: B 380 TYR cc_start: 0.7500 (m-80) cc_final: 0.6980 (m-80) REVERT: B 408 LYS cc_start: 0.7284 (tttp) cc_final: 0.6832 (tptp) REVERT: B 409 LEU cc_start: 0.7846 (mt) cc_final: 0.7533 (mt) REVERT: B 568 ILE cc_start: 0.8124 (mm) cc_final: 0.7783 (pt) REVERT: B 891 ASN cc_start: 0.8744 (t0) cc_final: 0.8359 (t0) REVERT: C 105 ILE cc_start: 0.8192 (mt) cc_final: 0.7971 (mm) REVERT: C 168 MET cc_start: 0.5211 (tmm) cc_final: 0.4881 (tpp) REVERT: C 181 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: C 408 LYS cc_start: 0.7392 (tttp) cc_final: 0.6896 (tptp) outliers start: 62 outliers final: 42 residues processed: 325 average time/residue: 0.1503 time to fit residues: 79.5662 Evaluate side-chains 276 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 1034 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 285 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 297 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 131 optimal weight: 0.0970 chunk 293 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 209 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 600 ASN B 701 ASN B 953 ASN C 393 GLN C 587 ASN C 701 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116915 restraints weight = 39182.930| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.23 r_work: 0.3110 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25599 Z= 0.118 Angle : 0.559 8.875 34716 Z= 0.297 Chirality : 0.044 0.195 4113 Planarity : 0.005 0.056 4239 Dihedral : 4.469 24.746 3363 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 1.64 % Allowed : 7.93 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.20 (0.15), residues: 3108 helix: 2.03 (0.21), residues: 669 sheet: 0.93 (0.20), residues: 609 loop : -1.44 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 181 TYR 0.025 0.001 TYR C 405 PHE 0.016 0.001 PHE C 440 TRP 0.008 0.001 TRP B1086 HIS 0.012 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (25599) covalent geometry : angle 0.55886 / 0.30 (34716) hydrogen bonds : bond 0.04290 / 2.83 ( 1018) hydrogen bonds : angle 5.52721 / 3.87 ( 2802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7668 (m-80) cc_final: 0.7410 (m-80) REVERT: A 168 MET cc_start: 0.5230 (tmm) cc_final: 0.4942 (tpp) REVERT: A 319 LEU cc_start: 0.7318 (tt) cc_final: 0.7042 (tp) REVERT: A 405 TYR cc_start: 0.6696 (m-80) cc_final: 0.6351 (m-80) REVERT: A 408 LYS cc_start: 0.7381 (tttp) cc_final: 0.6888 (tptp) REVERT: A 576 PHE cc_start: 0.7872 (p90) cc_final: 0.7629 (p90) REVERT: B 168 MET cc_start: 0.4949 (tmm) cc_final: 0.4633 (tpp) REVERT: B 313 PHE cc_start: 0.6986 (m-80) cc_final: 0.6538 (m-10) REVERT: B 319 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6314 (tp) REVERT: B 408 LYS cc_start: 0.7254 (tttp) cc_final: 0.6816 (tptp) REVERT: B 568 ILE cc_start: 0.8064 (mm) cc_final: 0.7769 (pt) REVERT: B 891 ASN cc_start: 0.8695 (t0) cc_final: 0.8371 (t0) REVERT: C 58 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: C 105 ILE cc_start: 0.8164 (mt) cc_final: 0.7927 (mm) REVERT: C 168 MET cc_start: 0.5231 (tmm) cc_final: 0.4922 (tpp) REVERT: C 181 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7391 (mtm-85) REVERT: C 408 LYS cc_start: 0.7359 (tttp) cc_final: 0.6858 (tptp) REVERT: C 448 PHE cc_start: 0.6724 (m-80) cc_final: 0.6503 (m-80) outliers start: 45 outliers final: 34 residues processed: 295 average time/residue: 0.1509 time to fit residues: 72.6082 Evaluate side-chains 271 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1034 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 9.9990 chunk 234 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 378 ASN C 434 ASN C 490 GLN C 524 ASN C 587 ASN C1055 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116956 restraints weight = 39149.022| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.23 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25599 Z= 0.122 Angle : 0.543 7.736 34716 Z= 0.288 Chirality : 0.043 0.171 4113 Planarity : 0.004 0.058 4239 Dihedral : 4.344 25.560 3363 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.04 % Allowed : 8.22 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.19 (0.15), residues: 3108 helix: 1.95 (0.21), residues: 687 sheet: 0.85 (0.20), residues: 615 loop : -1.41 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 181 TYR 0.021 0.001 TYR B 161 PHE 0.024 0.001 PHE B 474 TRP 0.007 0.001 TRP A 420 HIS 0.010 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (25599) covalent geometry : angle 0.54343 / 0.29 (34716) hydrogen bonds : bond 0.04195 / 2.76 ( 1018) hydrogen bonds : angle 5.41255 / 3.79 ( 2802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7693 (m-80) cc_final: 0.7468 (m-80) REVERT: A 168 MET cc_start: 0.5213 (tmm) cc_final: 0.4945 (tpp) REVERT: A 319 LEU cc_start: 0.7357 (tt) cc_final: 0.6918 (tp) REVERT: A 345 CYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 405 TYR cc_start: 0.6716 (m-80) cc_final: 0.6348 (m-80) REVERT: A 408 LYS cc_start: 0.7386 (tttp) cc_final: 0.6920 (tptp) REVERT: A 576 PHE cc_start: 0.7856 (p90) cc_final: 0.7604 (p90) REVERT: B 64 TRP cc_start: 0.7594 (t60) cc_final: 0.7262 (t60) REVERT: B 168 MET cc_start: 0.4807 (tmm) cc_final: 0.4529 (tpp) REVERT: B 212 SER cc_start: 0.8453 (m) cc_final: 0.8168 (p) REVERT: B 313 PHE cc_start: 0.7028 (m-80) cc_final: 0.6667 (m-10) REVERT: B 319 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6279 (tp) REVERT: B 362 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7648 (ptmt) REVERT: B 408 LYS cc_start: 0.7222 (tttp) cc_final: 0.6805 (tptp) REVERT: B 568 ILE cc_start: 0.8092 (mm) cc_final: 0.7766 (pt) REVERT: B 891 ASN cc_start: 0.8627 (t0) cc_final: 0.8328 (t0) REVERT: C 58 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: C 105 ILE cc_start: 0.8212 (mt) cc_final: 0.7984 (mm) REVERT: C 168 MET cc_start: 0.5148 (tmm) cc_final: 0.4794 (tpp) REVERT: C 362 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7643 (ptmt) REVERT: C 408 LYS cc_start: 0.7374 (tttp) cc_final: 0.6884 (tptp) REVERT: C 448 PHE cc_start: 0.6803 (m-80) cc_final: 0.6543 (m-80) outliers start: 56 outliers final: 35 residues processed: 283 average time/residue: 0.1506 time to fit residues: 70.0772 Evaluate side-chains 264 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 262 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 230 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 393 GLN C 490 GLN C 587 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN C1055 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.153243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114679 restraints weight = 39317.743| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.23 r_work: 0.3068 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25599 Z= 0.201 Angle : 0.604 7.631 34716 Z= 0.318 Chirality : 0.045 0.195 4113 Planarity : 0.005 0.061 4239 Dihedral : 4.611 26.446 3363 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.04 % Allowed : 8.66 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.48 (0.15), residues: 3108 helix: 1.58 (0.20), residues: 699 sheet: 0.76 (0.21), residues: 561 loop : -1.53 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 181 TYR 0.030 0.002 TYR C 405 PHE 0.028 0.002 PHE B 474 TRP 0.012 0.001 TRP C 870 HIS 0.009 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (25599) covalent geometry : angle 0.60355 / 0.32 (34716) hydrogen bonds : bond 0.04910 / 3.24 ( 1018) hydrogen bonds : angle 5.61574 / 3.93 ( 2802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7503 (m-80) cc_final: 0.7300 (m-80) REVERT: A 168 MET cc_start: 0.5237 (tmm) cc_final: 0.4986 (tpp) REVERT: A 345 CYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 362 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7583 (ptmt) REVERT: A 408 LYS cc_start: 0.7377 (tttp) cc_final: 0.6868 (tptp) REVERT: A 576 PHE cc_start: 0.7687 (p90) cc_final: 0.7376 (p90) REVERT: B 64 TRP cc_start: 0.7600 (t60) cc_final: 0.7313 (t60) REVERT: B 168 MET cc_start: 0.4847 (tmm) cc_final: 0.4576 (tpp) REVERT: B 212 SER cc_start: 0.8424 (m) cc_final: 0.8107 (p) REVERT: B 313 PHE cc_start: 0.6902 (m-80) cc_final: 0.6633 (m-10) REVERT: B 319 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6136 (tp) REVERT: B 345 CYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7662 (p) REVERT: B 362 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7638 (ptmt) REVERT: B 408 LYS cc_start: 0.7265 (tttp) cc_final: 0.6806 (tptp) REVERT: B 568 ILE cc_start: 0.8100 (mm) cc_final: 0.7713 (pt) REVERT: B 891 ASN cc_start: 0.8371 (t0) cc_final: 0.8009 (t0) REVERT: C 58 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: C 105 ILE cc_start: 0.8219 (mt) cc_final: 0.7955 (mm) REVERT: C 345 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 362 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7712 (ptmt) REVERT: C 408 LYS cc_start: 0.7345 (tttp) cc_final: 0.6912 (tptp) outliers start: 56 outliers final: 39 residues processed: 273 average time/residue: 0.1417 time to fit residues: 64.2220 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 0.4980 chunk 108 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 490 GLN C 587 ASN C 748 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117308 restraints weight = 39047.122| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.29 r_work: 0.3099 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25599 Z= 0.115 Angle : 0.538 7.573 34716 Z= 0.286 Chirality : 0.043 0.178 4113 Planarity : 0.004 0.067 4239 Dihedral : 4.324 26.170 3363 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.89 % Allowed : 9.10 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.36 (0.15), residues: 3108 helix: 1.81 (0.21), residues: 699 sheet: 0.75 (0.21), residues: 570 loop : -1.48 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 181 TYR 0.021 0.001 TYR A 888 PHE 0.021 0.001 PHE B 474 TRP 0.008 0.001 TRP B1086 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (25599) covalent geometry : angle 0.53844 / 0.29 (34716) hydrogen bonds : bond 0.04109 / 2.70 ( 1018) hydrogen bonds : angle 5.32663 / 3.72 ( 2802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5255 (tmm) cc_final: 0.5005 (tpp) REVERT: A 345 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 362 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7634 (ptmt) REVERT: A 408 LYS cc_start: 0.7398 (tttp) cc_final: 0.6892 (tptp) REVERT: A 576 PHE cc_start: 0.7697 (p90) cc_final: 0.7387 (p90) REVERT: B 64 TRP cc_start: 0.7542 (t60) cc_final: 0.7250 (t60) REVERT: B 168 MET cc_start: 0.4826 (tmm) cc_final: 0.4553 (tpp) REVERT: B 212 SER cc_start: 0.8433 (m) cc_final: 0.8135 (p) REVERT: B 319 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6094 (tp) REVERT: B 327 ASN cc_start: 0.6626 (t0) cc_final: 0.6410 (t0) REVERT: B 345 CYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 362 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7673 (ptmt) REVERT: B 408 LYS cc_start: 0.7269 (tttp) cc_final: 0.6834 (tptp) REVERT: B 568 ILE cc_start: 0.8099 (mm) cc_final: 0.7738 (pt) REVERT: B 891 ASN cc_start: 0.8329 (t0) cc_final: 0.8013 (t0) REVERT: C 32 PHE cc_start: 0.7306 (m-80) cc_final: 0.7074 (m-10) REVERT: C 58 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: C 105 ILE cc_start: 0.8208 (mt) cc_final: 0.7933 (mm) REVERT: C 345 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 362 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7706 (ptmt) REVERT: C 408 LYS cc_start: 0.7320 (tttp) cc_final: 0.6926 (tptp) REVERT: C 448 PHE cc_start: 0.6666 (m-80) cc_final: 0.6446 (m-80) outliers start: 52 outliers final: 37 residues processed: 272 average time/residue: 0.1432 time to fit residues: 64.0954 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 617 TRP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 145 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 266 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 490 GLN C 587 ASN C 639 HIS ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.152638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114233 restraints weight = 39112.438| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.21 r_work: 0.3058 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25599 Z= 0.217 Angle : 0.623 7.509 34716 Z= 0.327 Chirality : 0.046 0.201 4113 Planarity : 0.005 0.070 4239 Dihedral : 4.691 26.985 3363 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.00 % Allowed : 9.02 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 3108 helix: 1.52 (0.20), residues: 699 sheet: 0.63 (0.22), residues: 558 loop : -1.68 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 181 TYR 0.028 0.002 TYR A 888 PHE 0.022 0.002 PHE B 474 TRP 0.013 0.001 TRP C 870 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (25599) covalent geometry : angle 0.62292 / 0.33 (34716) hydrogen bonds : bond 0.05056 / 3.33 ( 1018) hydrogen bonds : angle 5.61689 / 3.93 ( 2802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5312 (tmm) cc_final: 0.5069 (tpp) REVERT: A 345 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7749 (p) REVERT: A 362 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7629 (ptmt) REVERT: A 408 LYS cc_start: 0.7548 (tttp) cc_final: 0.6997 (tptp) REVERT: A 576 PHE cc_start: 0.7696 (p90) cc_final: 0.7378 (p90) REVERT: A 617 TRP cc_start: 0.5427 (t-100) cc_final: 0.5207 (t-100) REVERT: B 64 TRP cc_start: 0.7623 (t60) cc_final: 0.7402 (t60) REVERT: B 168 MET cc_start: 0.4891 (tmm) cc_final: 0.4617 (tpp) REVERT: B 212 SER cc_start: 0.8427 (m) cc_final: 0.8121 (p) REVERT: B 319 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.5943 (tp) REVERT: B 327 ASN cc_start: 0.6673 (t0) cc_final: 0.6441 (t0) REVERT: B 345 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7687 (p) REVERT: B 362 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7671 (ptmt) REVERT: B 408 LYS cc_start: 0.7390 (tttp) cc_final: 0.6952 (tptp) REVERT: B 891 ASN cc_start: 0.8363 (t0) cc_final: 0.7986 (t0) REVERT: C 58 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8282 (m-10) REVERT: C 105 ILE cc_start: 0.8228 (mt) cc_final: 0.7967 (mm) REVERT: C 345 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 362 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7826 (ptpp) REVERT: C 408 LYS cc_start: 0.7380 (tttp) cc_final: 0.7009 (tptp) REVERT: C 448 PHE cc_start: 0.6860 (m-80) cc_final: 0.6590 (m-80) outliers start: 55 outliers final: 41 residues processed: 263 average time/residue: 0.1484 time to fit residues: 63.8633 Evaluate side-chains 253 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 953 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 587 ASN B 701 ASN C 587 ASN C 701 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112506 restraints weight = 39192.638| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.03 r_work: 0.3105 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25599 Z= 0.121 Angle : 0.550 7.603 34716 Z= 0.291 Chirality : 0.043 0.189 4113 Planarity : 0.005 0.076 4239 Dihedral : 4.403 26.581 3363 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.82 % Allowed : 9.46 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.54 (0.15), residues: 3108 helix: 1.73 (0.21), residues: 702 sheet: 0.60 (0.21), residues: 573 loop : -1.63 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 181 TYR 0.025 0.001 TYR B 161 PHE 0.033 0.001 PHE A 954 TRP 0.008 0.001 TRP C1086 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (25599) covalent geometry : angle 0.55039 / 0.29 (34716) hydrogen bonds : bond 0.04200 / 2.75 ( 1018) hydrogen bonds : angle 5.33710 / 3.72 ( 2802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5392 (tmm) cc_final: 0.5120 (tpp) REVERT: A 345 CYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 408 LYS cc_start: 0.7585 (tttp) cc_final: 0.7028 (tptp) REVERT: A 576 PHE cc_start: 0.7742 (p90) cc_final: 0.7408 (p90) REVERT: A 617 TRP cc_start: 0.5567 (t-100) cc_final: 0.5136 (t-100) REVERT: B 64 TRP cc_start: 0.7591 (t60) cc_final: 0.7370 (t60) REVERT: B 168 MET cc_start: 0.4878 (tmm) cc_final: 0.4586 (tpp) REVERT: B 212 SER cc_start: 0.8438 (m) cc_final: 0.8164 (p) REVERT: B 319 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.5818 (tp) REVERT: B 327 ASN cc_start: 0.6779 (t0) cc_final: 0.6535 (t0) REVERT: B 345 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7628 (p) REVERT: B 362 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7694 (ptmt) REVERT: B 408 LYS cc_start: 0.7451 (tttp) cc_final: 0.6985 (tptp) REVERT: B 701 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 891 ASN cc_start: 0.8555 (t0) cc_final: 0.8235 (t0) REVERT: C 58 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: C 105 ILE cc_start: 0.8230 (mt) cc_final: 0.7968 (mm) REVERT: C 345 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7372 (p) REVERT: C 362 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7717 (ptmt) REVERT: C 408 LYS cc_start: 0.7482 (tttp) cc_final: 0.7079 (tptp) REVERT: C 448 PHE cc_start: 0.6775 (m-80) cc_final: 0.6531 (m-80) outliers start: 50 outliers final: 36 residues processed: 257 average time/residue: 0.1497 time to fit residues: 62.8890 Evaluate side-chains 252 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 617 TRP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 127 optimal weight: 0.8980 chunk 297 optimal weight: 0.8980 chunk 56 optimal weight: 0.0570 chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 587 ASN C 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115579 restraints weight = 39046.917| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.14 r_work: 0.3112 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25599 Z= 0.136 Angle : 0.552 7.553 34716 Z= 0.292 Chirality : 0.043 0.186 4113 Planarity : 0.005 0.078 4239 Dihedral : 4.387 27.136 3363 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.67 % Allowed : 9.68 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.54 (0.15), residues: 3108 helix: 1.76 (0.21), residues: 702 sheet: 0.60 (0.21), residues: 573 loop : -1.64 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 181 TYR 0.021 0.001 TYR B1051 PHE 0.022 0.001 PHE A 92 TRP 0.010 0.001 TRP A 143 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (25599) covalent geometry : angle 0.55246 / 0.29 (34716) hydrogen bonds : bond 0.04261 / 2.80 ( 1018) hydrogen bonds : angle 5.30436 / 3.70 ( 2802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.3075 (ttt) cc_final: 0.2748 (tmm) REVERT: A 168 MET cc_start: 0.5452 (tmm) cc_final: 0.5192 (tpp) REVERT: A 341 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7302 (ttm-80) REVERT: A 345 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 408 LYS cc_start: 0.7577 (tttp) cc_final: 0.7037 (tptp) REVERT: A 576 PHE cc_start: 0.7772 (p90) cc_final: 0.7425 (p90) REVERT: A 617 TRP cc_start: 0.5606 (t-100) cc_final: 0.5149 (t-100) REVERT: B 168 MET cc_start: 0.4858 (tmm) cc_final: 0.4579 (tpp) REVERT: B 212 SER cc_start: 0.8373 (m) cc_final: 0.8123 (p) REVERT: B 327 ASN cc_start: 0.6834 (t0) cc_final: 0.6601 (t0) REVERT: B 345 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 362 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7655 (ptmt) REVERT: B 408 LYS cc_start: 0.7429 (tttp) cc_final: 0.6959 (tptp) REVERT: B 891 ASN cc_start: 0.8549 (t0) cc_final: 0.8235 (t0) REVERT: C 32 PHE cc_start: 0.7394 (m-80) cc_final: 0.7133 (m-10) REVERT: C 58 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: C 105 ILE cc_start: 0.8240 (mt) cc_final: 0.7980 (mm) REVERT: C 345 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7362 (p) REVERT: C 362 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7704 (ptmt) REVERT: C 408 LYS cc_start: 0.7482 (tttp) cc_final: 0.7152 (tptp) REVERT: C 448 PHE cc_start: 0.6774 (m-80) cc_final: 0.6513 (m-80) outliers start: 46 outliers final: 36 residues processed: 244 average time/residue: 0.1494 time to fit residues: 60.1851 Evaluate side-chains 248 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 617 TRP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 301 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 251 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116037 restraints weight = 38792.848| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.12 r_work: 0.3098 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25599 Z= 0.138 Angle : 0.551 7.595 34716 Z= 0.290 Chirality : 0.044 0.185 4113 Planarity : 0.005 0.078 4239 Dihedral : 4.374 28.028 3363 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.82 % Allowed : 9.57 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.57 (0.15), residues: 3108 helix: 1.70 (0.20), residues: 708 sheet: 0.64 (0.21), residues: 570 loop : -1.67 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 181 TYR 0.020 0.001 TYR B1051 PHE 0.018 0.001 PHE B 474 TRP 0.011 0.001 TRP C 143 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (25599) covalent geometry : angle 0.55055 / 0.29 (34716) hydrogen bonds : bond 0.04266 / 2.81 ( 1018) hydrogen bonds : angle 5.28713 / 3.69 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6351.55 seconds wall clock time: 109 minutes 58.73 seconds (6598.73 seconds total)