Starting phenix.real_space_refine on Mon Aug 25 04:02:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_29454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_29454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_29454.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_29454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu7_29454/08_2025/8fu7_29454.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.81, per 1000 atoms: 0.19 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.07 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: 5.13 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 15552 20.53 - 41.06: 365 41.06 - 61.60: 86 61.60 - 82.13: 28 82.13 - 102.66: 7 Dihedral angle restraints: 16038 sinusoidal: 6903 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 16035 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: 0.02 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: 6.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.220 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 10.159 102.659 10164 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 aren 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 covalent geometry : bond 0.01241 (25599) covalent geometry : angle 1.29703 (34716) hydrogen bonds : bond 0.17019 ( 1018) hydrogen bonds : angle 8.13780 ( 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 : 0.877 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: 0.1751 time to fit residues: 130.1407 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 : 0.761 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 198 HIS B 198 HIS B 587 ASN B 701 ASN B 748 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118413 restraints weight = 39433.015| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.32 r_work: 0.3126 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25599 Z= 0.151 Angle : 0.628 8.008 34716 Z= 0.339 Chirality : 0.046 0.226 4113 Planarity : 0.005 0.047 4239 Dihedral : 5.379 45.016 4515 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.08 % Favored : 93.79 % Rotamer: Outliers : 1.27 % Allowed : 4.37 % 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 aren not related in a simple way. whole: 0.02 (0.15), residues: 3108 helix: 1.86 (0.21), residues: 666 sheet: 1.25 (0.21), residues: 582 loop : -1.17 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 228 TYR 0.023 0.002 TYR B 161 PHE 0.033 0.002 PHE B 135 TRP 0.008 0.001 TRP A 420 HIS 0.020 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00321 (25599) covalent geometry : angle 0.62778 (34716) hydrogen bonds : bond 0.05266 ( 1018) hydrogen bonds : angle 6.13095 ( 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 367 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 332 time to evaluate : 0.904 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: 0.7455 (m-80) cc_final: 0.7043 (m-80) REVERT: A 130 VAL cc_start: 0.7638 (t) cc_final: 0.7427 (t) REVERT: A 196 SER cc_start: 0.8650 (p) cc_final: 0.8366 (m) REVERT: A 319 LEU cc_start: 0.6687 (mt) cc_final: 0.6355 (tp) REVERT: A 380 TYR cc_start: 0.7335 (m-80) cc_final: 0.7013 (m-80) REVERT: A 408 LYS cc_start: 0.7051 (tttp) cc_final: 0.6739 (tptp) REVERT: B 181 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: B 196 SER cc_start: 0.8737 (p) cc_final: 0.8427 (m) REVERT: B 313 PHE cc_start: 0.6957 (m-80) cc_final: 0.6715 (m-10) REVERT: B 319 LEU cc_start: 0.6850 (mm) cc_final: 0.6440 (tp) REVERT: B 380 TYR cc_start: 0.7423 (m-80) cc_final: 0.7054 (m-80) REVERT: B 408 LYS cc_start: 0.7034 (tttp) cc_final: 0.6633 (tptp) REVERT: B 568 ILE cc_start: 0.8262 (mm) cc_final: 0.7963 (pt) REVERT: B 891 ASN cc_start: 0.8360 (t0) cc_final: 0.8075 (t0) REVERT: C 105 ILE cc_start: 0.8013 (mt) cc_final: 0.7757 (mm) REVERT: C 125 ASN cc_start: 0.6904 (m-40) cc_final: 0.6642 (m-40) REVERT: C 181 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7386 (mtm-85) REVERT: C 196 SER cc_start: 0.8706 (p) cc_final: 0.8411 (m) REVERT: C 319 LEU cc_start: 0.6698 (mt) cc_final: 0.6447 (tp) REVERT: C 408 LYS cc_start: 0.7125 (tttp) cc_final: 0.6679 (tptp) REVERT: C 448 PHE cc_start: 0.6755 (m-80) cc_final: 0.6271 (m-80) outliers start: 35 outliers final: 20 residues processed: 358 average time/residue: 0.1470 time to fit residues: 84.6268 Evaluate side-chains 269 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 54 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 393 GLN A1032 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN B1032 HIS C 587 ASN C 701 ASN C1032 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116716 restraints weight = 39318.565| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.24 r_work: 0.3109 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25599 Z= 0.149 Angle : 0.585 7.599 34716 Z= 0.312 Chirality : 0.045 0.224 4113 Planarity : 0.005 0.053 4239 Dihedral : 5.241 44.069 4515 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.82 % Allowed : 6.22 % Favored : 91.96 % 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 aren not related in a simple way. whole: -0.12 (0.15), residues: 3108 helix: 1.97 (0.21), residues: 672 sheet: 1.01 (0.21), residues: 609 loop : -1.34 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 228 TYR 0.030 0.001 TYR A 161 PHE 0.029 0.002 PHE A 474 TRP 0.013 0.001 TRP B1086 HIS 0.016 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00334 (25599) covalent geometry : angle 0.58533 (34716) hydrogen bonds : bond 0.04749 ( 1018) hydrogen bonds : angle 5.68221 ( 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 321 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7559 (m-80) cc_final: 0.7252 (m-80) REVERT: A 168 MET cc_start: 0.5064 (tmm) cc_final: 0.4769 (tpp) REVERT: A 380 TYR cc_start: 0.7412 (m-80) cc_final: 0.6969 (m-80) REVERT: A 408 LYS cc_start: 0.7136 (tttp) cc_final: 0.6754 (tptp) REVERT: B 168 MET cc_start: 0.4888 (tmm) cc_final: 0.4602 (tpp) REVERT: B 181 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: B 196 SER cc_start: 0.8715 (p) cc_final: 0.8473 (m) REVERT: B 319 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6325 (tp) REVERT: B 408 LYS cc_start: 0.7134 (tttp) cc_final: 0.6697 (tptp) REVERT: B 568 ILE cc_start: 0.8069 (mm) cc_final: 0.7855 (pt) REVERT: B 891 ASN cc_start: 0.8408 (t0) cc_final: 0.8043 (t0) REVERT: C 48 LEU cc_start: 0.8515 (mt) cc_final: 0.8304 (mp) REVERT: C 105 ILE cc_start: 0.8073 (mt) cc_final: 0.7826 (mm) REVERT: C 168 MET cc_start: 0.5102 (tmm) cc_final: 0.4823 (tpp) REVERT: C 181 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7266 (mtm-85) REVERT: C 196 SER cc_start: 0.8738 (p) cc_final: 0.8507 (m) REVERT: C 408 LYS cc_start: 0.7242 (tttp) cc_final: 0.6763 (tptp) outliers start: 50 outliers final: 34 residues processed: 307 average time/residue: 0.1514 time to fit residues: 75.8210 Evaluate side-chains 274 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 310 ILE Chi-restraints excluded: chain A residue 318 ASN 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 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 319 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR 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 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 498 SER 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 788 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 285 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 600 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 639 HIS B 701 ASN C 230 GLN C 393 GLN C 434 ASN C 490 GLN C 587 ASN C 600 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113691 restraints weight = 39181.568| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.21 r_work: 0.3059 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25599 Z= 0.224 Angle : 0.636 8.810 34716 Z= 0.337 Chirality : 0.047 0.215 4113 Planarity : 0.005 0.049 4239 Dihedral : 5.662 37.471 4515 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 2.11 % Allowed : 7.42 % Favored : 90.47 % 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 aren not related in a simple way. whole: -0.48 (0.15), residues: 3108 helix: 1.79 (0.21), residues: 663 sheet: 0.77 (0.21), residues: 579 loop : -1.57 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 181 TYR 0.022 0.002 TYR C 161 PHE 0.019 0.002 PHE B 135 TRP 0.018 0.001 TRP C 870 HIS 0.011 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00529 (25599) covalent geometry : angle 0.63637 (34716) hydrogen bonds : bond 0.05321 ( 1018) hydrogen bonds : angle 5.81314 ( 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 309 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5250 (tmm) cc_final: 0.4981 (tpp) REVERT: A 380 TYR cc_start: 0.7592 (m-80) cc_final: 0.7097 (m-80) REVERT: A 408 LYS cc_start: 0.7423 (tttp) cc_final: 0.6915 (tptp) REVERT: A 576 PHE cc_start: 0.7891 (p90) cc_final: 0.7619 (p90) REVERT: B 32 PHE cc_start: 0.7563 (m-80) cc_final: 0.7316 (m-80) REVERT: B 168 MET cc_start: 0.5015 (tmm) cc_final: 0.4673 (tpp) REVERT: B 212 SER cc_start: 0.8485 (m) cc_final: 0.8182 (p) REVERT: B 319 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6287 (tp) REVERT: B 408 LYS cc_start: 0.7315 (tttp) cc_final: 0.6858 (tptp) REVERT: B 568 ILE cc_start: 0.8132 (mm) cc_final: 0.7771 (pt) REVERT: B 793 PRO cc_start: 0.4871 (Cg_endo) cc_final: 0.4671 (Cg_exo) REVERT: B 891 ASN cc_start: 0.8699 (t0) cc_final: 0.8322 (t0) REVERT: C 58 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8284 (m-10) REVERT: C 105 ILE cc_start: 0.8218 (mt) cc_final: 0.7961 (mm) REVERT: C 168 MET cc_start: 0.5225 (tmm) cc_final: 0.4912 (tpp) REVERT: C 408 LYS cc_start: 0.7410 (tttp) cc_final: 0.6905 (tptp) REVERT: C 448 PHE cc_start: 0.6792 (m-80) cc_final: 0.6549 (m-80) outliers start: 58 outliers final: 39 residues processed: 303 average time/residue: 0.1471 time to fit residues: 72.6711 Evaluate side-chains 266 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 196 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 498 SER 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 788 GLN Chi-restraints excluded: chain B residue 58 PHE 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 587 ASN 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 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 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 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 587 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 279 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116417 restraints weight = 39099.888| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.18 r_work: 0.3109 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25599 Z= 0.119 Angle : 0.549 8.887 34716 Z= 0.292 Chirality : 0.043 0.172 4113 Planarity : 0.005 0.059 4239 Dihedral : 5.216 42.364 4515 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.75 % Allowed : 8.48 % Favored : 89.77 % 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 aren not related in a simple way. whole: -0.30 (0.15), residues: 3108 helix: 1.91 (0.21), residues: 687 sheet: 0.81 (0.21), residues: 567 loop : -1.44 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 181 TYR 0.033 0.001 TYR C 405 PHE 0.021 0.001 PHE B 474 TRP 0.009 0.001 TRP C1086 HIS 0.010 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00256 (25599) covalent geometry : angle 0.54879 (34716) hydrogen bonds : bond 0.04250 ( 1018) hydrogen bonds : angle 5.46006 ( 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 302 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7613 (m-80) cc_final: 0.7389 (m-80) REVERT: A 168 MET cc_start: 0.5311 (tmm) cc_final: 0.5033 (tpp) REVERT: A 345 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 408 LYS cc_start: 0.7409 (tttp) cc_final: 0.6916 (tptp) REVERT: A 576 PHE cc_start: 0.7857 (p90) cc_final: 0.7577 (p90) REVERT: A 961 LEU cc_start: 0.8279 (mt) cc_final: 0.8049 (tp) REVERT: B 32 PHE cc_start: 0.7706 (m-80) cc_final: 0.7485 (m-80) REVERT: B 64 TRP cc_start: 0.7587 (t60) cc_final: 0.7259 (t60) REVERT: B 168 MET cc_start: 0.4961 (tmm) cc_final: 0.4639 (tpp) REVERT: B 212 SER cc_start: 0.8477 (m) cc_final: 0.8177 (p) REVERT: B 319 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6159 (tp) REVERT: B 345 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 362 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7719 (ptmt) REVERT: B 408 LYS cc_start: 0.7358 (tttp) cc_final: 0.6902 (tptp) REVERT: B 448 PHE cc_start: 0.6835 (m-80) cc_final: 0.6593 (m-80) REVERT: B 568 ILE cc_start: 0.8102 (mm) cc_final: 0.7764 (pt) REVERT: B 891 ASN cc_start: 0.8630 (t0) cc_final: 0.8334 (t0) REVERT: C 58 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: C 105 ILE cc_start: 0.8223 (mt) cc_final: 0.7959 (mm) REVERT: C 168 MET cc_start: 0.5044 (tmm) cc_final: 0.4832 (tpp) REVERT: C 345 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7494 (p) REVERT: C 408 LYS cc_start: 0.7401 (tttp) cc_final: 0.6878 (tptp) REVERT: C 448 PHE cc_start: 0.6786 (m-80) cc_final: 0.6523 (m-80) outliers start: 48 outliers final: 25 residues processed: 294 average time/residue: 0.1359 time to fit residues: 65.3916 Evaluate side-chains 265 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 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 884 MET Chi-restraints excluded: chain B residue 897 GLN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 262 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 230 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 154 optimal weight: 0.0570 chunk 184 optimal weight: 1.9990 chunk 214 optimal weight: 0.0030 chunk 284 optimal weight: 3.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN B 490 GLN C 587 ASN C 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118261 restraints weight = 39264.844| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.22 r_work: 0.3138 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25599 Z= 0.103 Angle : 0.522 7.948 34716 Z= 0.277 Chirality : 0.043 0.175 4113 Planarity : 0.004 0.061 4239 Dihedral : 4.605 33.508 4515 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.49 % Allowed : 8.95 % Favored : 89.56 % 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 aren not related in a simple way. whole: -0.23 (0.15), residues: 3108 helix: 1.89 (0.21), residues: 705 sheet: 0.73 (0.21), residues: 591 loop : -1.37 (0.15), residues: 1812 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 B 474 TRP 0.007 0.001 TRP A1086 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00209 (25599) covalent geometry : angle 0.52193 (34716) hydrogen bonds : bond 0.03776 ( 1018) hydrogen bonds : angle 5.17139 ( 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 293 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5233 (tmm) cc_final: 0.4983 (tpp) REVERT: A 345 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7650 (p) REVERT: A 362 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7587 (ptmt) REVERT: A 408 LYS cc_start: 0.7351 (tttp) cc_final: 0.6864 (tptp) REVERT: A 493 ARG cc_start: 0.4365 (mmt90) cc_final: 0.4163 (mmt90) REVERT: A 576 PHE cc_start: 0.7660 (p90) cc_final: 0.7365 (p90) REVERT: A 587 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7242 (t160) REVERT: B 64 TRP cc_start: 0.7476 (t60) cc_final: 0.7183 (t60) REVERT: B 168 MET cc_start: 0.4923 (tmm) cc_final: 0.4584 (tpp) REVERT: B 212 SER cc_start: 0.8426 (m) cc_final: 0.8148 (p) REVERT: B 319 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6166 (tp) REVERT: B 345 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7632 (p) REVERT: B 362 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7638 (ptmt) REVERT: B 408 LYS cc_start: 0.7284 (tttp) cc_final: 0.6834 (tptp) REVERT: B 448 PHE cc_start: 0.6751 (m-80) cc_final: 0.6501 (m-80) REVERT: B 568 ILE cc_start: 0.8106 (mm) cc_final: 0.7765 (pt) REVERT: B 891 ASN cc_start: 0.8275 (t0) cc_final: 0.7962 (t0) REVERT: C 105 ILE cc_start: 0.8157 (mt) cc_final: 0.7911 (mm) REVERT: C 168 MET cc_start: 0.5019 (tmm) cc_final: 0.4791 (tpp) REVERT: C 362 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7827 (ptpp) REVERT: C 408 LYS cc_start: 0.7354 (tttp) cc_final: 0.6814 (tptp) REVERT: C 448 PHE cc_start: 0.6625 (m-80) cc_final: 0.6359 (m-80) outliers start: 41 outliers final: 27 residues processed: 281 average time/residue: 0.1427 time to fit residues: 64.9731 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 393 GLN 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 884 MET Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 286 THR 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 977 ILE Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A1082 ASN B 490 GLN C 490 GLN C 587 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN C 919 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115304 restraints weight = 39006.313| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.21 r_work: 0.3093 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25599 Z= 0.177 Angle : 0.572 7.951 34716 Z= 0.302 Chirality : 0.044 0.179 4113 Planarity : 0.005 0.066 4239 Dihedral : 4.911 32.339 4515 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.82 % Allowed : 9.06 % Favored : 89.12 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3108 helix: 1.74 (0.20), residues: 702 sheet: 0.73 (0.21), residues: 573 loop : -1.53 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 181 TYR 0.031 0.002 TYR A 888 PHE 0.022 0.002 PHE B 576 TRP 0.010 0.001 TRP C 870 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00416 (25599) covalent geometry : angle 0.57225 (34716) hydrogen bonds : bond 0.04555 ( 1018) hydrogen bonds : angle 5.39980 ( 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 281 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5323 (tmm) cc_final: 0.5060 (tpp) REVERT: A 345 CYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7693 (p) REVERT: A 362 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7534 (ptmt) REVERT: A 408 LYS cc_start: 0.7480 (tttp) cc_final: 0.6954 (tptp) REVERT: A 576 PHE cc_start: 0.7795 (p90) cc_final: 0.7447 (p90) REVERT: B 64 TRP cc_start: 0.7648 (t60) cc_final: 0.7419 (t60) REVERT: B 168 MET cc_start: 0.4837 (tmm) cc_final: 0.4551 (tpp) REVERT: B 212 SER cc_start: 0.8443 (m) cc_final: 0.8153 (p) REVERT: B 345 CYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 362 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7703 (ptmt) REVERT: B 408 LYS cc_start: 0.7393 (tttp) cc_final: 0.6963 (tptp) REVERT: B 568 ILE cc_start: 0.8118 (mm) cc_final: 0.7736 (pt) REVERT: B 891 ASN cc_start: 0.8587 (t0) cc_final: 0.8269 (t0) REVERT: C 105 ILE cc_start: 0.8196 (mt) cc_final: 0.7935 (mm) REVERT: C 320 CYS cc_start: 0.5814 (m) cc_final: 0.4652 (m) REVERT: C 345 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7416 (p) REVERT: C 362 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7887 (ptpp) REVERT: C 408 LYS cc_start: 0.7403 (tttp) cc_final: 0.7018 (tptp) outliers start: 50 outliers final: 37 residues processed: 268 average time/residue: 0.1372 time to fit residues: 60.3845 Evaluate side-chains 259 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 587 ASN 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 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 318 ASN Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 393 GLN 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 977 ILE Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN 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 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 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 192 optimal weight: 0.0570 chunk 243 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN C 187 ASN C 587 ASN C 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115742 restraints weight = 39013.497| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.19 r_work: 0.3102 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25599 Z= 0.147 Angle : 0.553 8.287 34716 Z= 0.293 Chirality : 0.044 0.185 4113 Planarity : 0.005 0.071 4239 Dihedral : 4.877 32.934 4515 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.75 % Allowed : 9.46 % Favored : 88.79 % 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 aren not related in a simple way. whole: -0.46 (0.15), residues: 3108 helix: 1.71 (0.20), residues: 705 sheet: 0.71 (0.21), residues: 573 loop : -1.56 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 181 TYR 0.024 0.001 TYR A 888 PHE 0.026 0.002 PHE B 576 TRP 0.009 0.001 TRP A1086 HIS 0.008 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00336 (25599) covalent geometry : angle 0.55267 (34716) hydrogen bonds : bond 0.04365 ( 1018) hydrogen bonds : angle 5.34744 ( 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 271 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5377 (tmm) cc_final: 0.5116 (tpp) REVERT: A 345 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 362 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7551 (ptmt) REVERT: A 408 LYS cc_start: 0.7548 (tttp) cc_final: 0.6979 (tptp) REVERT: A 576 PHE cc_start: 0.7777 (p90) cc_final: 0.7423 (p90) REVERT: B 64 TRP cc_start: 0.7624 (t60) cc_final: 0.7396 (t60) REVERT: B 168 MET cc_start: 0.4886 (tmm) cc_final: 0.4606 (tpp) REVERT: B 212 SER cc_start: 0.8436 (m) cc_final: 0.8160 (p) REVERT: B 345 CYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 362 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7659 (ptmt) REVERT: B 408 LYS cc_start: 0.7477 (tttp) cc_final: 0.7002 (tptp) REVERT: B 448 PHE cc_start: 0.6813 (m-80) cc_final: 0.6521 (m-80) REVERT: B 568 ILE cc_start: 0.8106 (mm) cc_final: 0.7709 (pt) REVERT: B 891 ASN cc_start: 0.8601 (t0) cc_final: 0.8292 (t0) REVERT: C 105 ILE cc_start: 0.8212 (mt) cc_final: 0.7961 (mm) REVERT: C 320 CYS cc_start: 0.5874 (m) cc_final: 0.4698 (m) REVERT: C 345 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7478 (p) REVERT: C 362 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7716 (ptmt) REVERT: C 408 LYS cc_start: 0.7401 (tttp) cc_final: 0.7072 (tptp) REVERT: C 448 PHE cc_start: 0.6736 (m-80) cc_final: 0.6487 (m-80) outliers start: 48 outliers final: 37 residues processed: 261 average time/residue: 0.1416 time to fit residues: 60.9247 Evaluate side-chains 251 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 587 ASN 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 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 345 CYS Chi-restraints excluded: chain B residue 393 GLN 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 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 977 ILE Chi-restraints excluded: chain C residue 1082 ASN 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: 0.9980 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 ASN C 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116579 restraints weight = 39066.024| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.16 r_work: 0.3116 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25599 Z= 0.120 Angle : 0.532 8.512 34716 Z= 0.282 Chirality : 0.043 0.174 4113 Planarity : 0.004 0.076 4239 Dihedral : 4.677 31.338 4515 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.64 % Allowed : 9.61 % Favored : 88.76 % 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 aren not related in a simple way. whole: -0.41 (0.15), residues: 3108 helix: 1.76 (0.21), residues: 708 sheet: 0.73 (0.21), residues: 573 loop : -1.54 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 181 TYR 0.022 0.001 TYR B 161 PHE 0.026 0.001 PHE B 576 TRP 0.008 0.001 TRP A 143 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00264 (25599) covalent geometry : angle 0.53167 (34716) hydrogen bonds : bond 0.04082 ( 1018) hydrogen bonds : angle 5.23802 ( 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 260 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.3025 (ttt) cc_final: 0.2590 (tmm) REVERT: A 168 MET cc_start: 0.5408 (tmm) cc_final: 0.5157 (tpp) REVERT: A 345 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7661 (p) REVERT: A 362 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7548 (ptmt) REVERT: A 408 LYS cc_start: 0.7549 (tttp) cc_final: 0.6991 (tptp) REVERT: A 576 PHE cc_start: 0.7795 (p90) cc_final: 0.7481 (p90) REVERT: B 168 MET cc_start: 0.4879 (tmm) cc_final: 0.4606 (tpp) REVERT: B 212 SER cc_start: 0.8384 (m) cc_final: 0.8112 (p) REVERT: B 345 CYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7604 (p) REVERT: B 362 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7677 (ptmt) REVERT: B 408 LYS cc_start: 0.7440 (tttp) cc_final: 0.6954 (tptp) REVERT: B 448 PHE cc_start: 0.6767 (m-80) cc_final: 0.6491 (m-80) REVERT: B 568 ILE cc_start: 0.8093 (mm) cc_final: 0.7710 (pt) REVERT: B 891 ASN cc_start: 0.8551 (t0) cc_final: 0.8237 (t0) REVERT: C 105 ILE cc_start: 0.8220 (mt) cc_final: 0.7966 (mm) REVERT: C 320 CYS cc_start: 0.5805 (m) cc_final: 0.4698 (m) REVERT: C 345 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7510 (p) REVERT: C 362 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7692 (ptmt) REVERT: C 408 LYS cc_start: 0.7424 (tttp) cc_final: 0.7126 (tptp) REVERT: C 448 PHE cc_start: 0.6779 (m-80) cc_final: 0.6528 (m-80) outliers start: 45 outliers final: 37 residues processed: 249 average time/residue: 0.1442 time to fit residues: 58.5494 Evaluate side-chains 251 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 PHE 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 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 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 345 CYS Chi-restraints excluded: chain B residue 393 GLN 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 47 VAL 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 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 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 127 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 ASN C 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103561 restraints weight = 39107.100| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.23 r_work: 0.3077 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25599 Z= 0.122 Angle : 0.530 8.693 34716 Z= 0.281 Chirality : 0.043 0.168 4113 Planarity : 0.004 0.078 4239 Dihedral : 4.583 30.585 4515 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.64 % Allowed : 9.83 % Favored : 88.54 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3108 helix: 1.79 (0.21), residues: 708 sheet: 0.72 (0.21), residues: 573 loop : -1.55 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 181 TYR 0.021 0.001 TYR B1051 PHE 0.026 0.001 PHE B 576 TRP 0.008 0.001 TRP C 143 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00270 (25599) covalent geometry : angle 0.53001 (34716) hydrogen bonds : bond 0.04043 ( 1018) hydrogen bonds : angle 5.18102 ( 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 264 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.3084 (ttt) cc_final: 0.2643 (tmm) REVERT: A 168 MET cc_start: 0.5475 (tmm) cc_final: 0.5208 (tpp) REVERT: A 345 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7533 (p) REVERT: A 362 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7714 (ptmt) REVERT: A 408 LYS cc_start: 0.7593 (tttp) cc_final: 0.7018 (tptp) REVERT: A 576 PHE cc_start: 0.7709 (p90) cc_final: 0.7387 (p90) REVERT: B 168 MET cc_start: 0.4976 (tmm) cc_final: 0.4686 (tpp) REVERT: B 212 SER cc_start: 0.8309 (m) cc_final: 0.8014 (p) REVERT: B 345 CYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7521 (p) REVERT: B 362 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7808 (ptmt) REVERT: B 408 LYS cc_start: 0.7504 (tttp) cc_final: 0.6982 (tptp) REVERT: B 448 PHE cc_start: 0.6912 (m-80) cc_final: 0.6608 (m-80) REVERT: B 568 ILE cc_start: 0.8109 (mm) cc_final: 0.7695 (pt) REVERT: B 891 ASN cc_start: 0.8606 (t0) cc_final: 0.8285 (t0) REVERT: C 105 ILE cc_start: 0.8162 (mt) cc_final: 0.7875 (mm) REVERT: C 320 CYS cc_start: 0.5745 (m) cc_final: 0.4605 (m) REVERT: C 345 CYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7433 (p) REVERT: C 362 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7790 (ptmt) REVERT: C 408 LYS cc_start: 0.7457 (tttp) cc_final: 0.7108 (tptp) REVERT: C 448 PHE cc_start: 0.6855 (m-80) cc_final: 0.6572 (m-80) outliers start: 45 outliers final: 37 residues processed: 253 average time/residue: 0.1356 time to fit residues: 56.4591 Evaluate side-chains 249 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL 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 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 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 393 GLN 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 47 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN A 639 HIS A 674 GLN C 639 HIS C 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113835 restraints weight = 38932.121| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.14 r_work: 0.3070 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 25599 Z= 0.216 Angle : 0.611 9.420 34716 Z= 0.323 Chirality : 0.046 0.203 4113 Planarity : 0.005 0.079 4239 Dihedral : 5.326 36.586 4515 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.56 % Allowed : 10.01 % Favored : 88.43 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 3108 helix: 1.48 (0.20), residues: 705 sheet: 0.61 (0.21), residues: 555 loop : -1.73 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 181 TYR 0.029 0.002 TYR A 888 PHE 0.030 0.002 PHE B 576 TRP 0.015 0.001 TRP A 420 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00513 (25599) covalent geometry : angle 0.61144 (34716) hydrogen bonds : bond 0.05040 ( 1018) hydrogen bonds : angle 5.57716 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6014.19 seconds wall clock time: 103 minutes 55.87 seconds (6235.87 seconds total)