Starting phenix.real_space_refine on Sat May 24 05:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu7_29454/05_2025/8fu7_29454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu7_29454/05_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_29454/05_2025/8fu7_29454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu7_29454/05_2025/8fu7_29454.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu7_29454/05_2025/8fu7_29454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu7_29454/05_2025/8fu7_29454.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 38, 'ASP:plan': 45} 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: {'GLU:plan': 38, 'ASP:plan': 45} 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: {'GLU:plan': 38, 'ASP:plan': 45} 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: 16.49, per 1000 atoms: 0.66 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: 5.84 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.75 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: 12.41 Time building geometry restraints manager: 6.88 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: 0.09 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: 4.760 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: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 61.240 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.110 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.004 TRP C 64 HIS 0.004 0.001 HIS A 137 PHE 0.025 0.003 PHE A 474 TYR 0.038 0.005 TYR B 437 ARG 0.003 0.000 ARG A 984 Details of bonding type rmsd hydrogen bonds : bond 0.17019 ( 1018) hydrogen bonds : angle 8.13780 ( 2802) covalent geometry : bond 0.01241 (25599) covalent geometry : angle 1.29703 (34716) *********************** 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 : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6990 (m-40) cc_final: 0.6762 (t0) REVERT: A 319 LEU cc_start: 0.6677 (mt) cc_final: 0.6216 (tp) REVERT: A 344 ASN cc_start: 0.8066 (m-40) cc_final: 0.7841 (m-40) REVERT: A 352 LEU cc_start: 0.8499 (mt) cc_final: 0.8220 (mp) REVERT: A 360 THR cc_start: 0.6356 (t) cc_final: 0.6143 (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: 0.6718 (m-80) REVERT: A 392 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7426 (ppt170) REVERT: A 405 TYR cc_start: 0.7580 (m-80) cc_final: 0.6997 (m-80) REVERT: A 408 LYS cc_start: 0.6716 (tttp) cc_final: 0.6494 (tptp) REVERT: A 497 LEU cc_start: 0.8464 (mt) cc_final: 0.8256 (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: 0.6469 (p0) REVERT: A 919 GLN cc_start: 0.6964 (mt0) cc_final: 0.6635 (mt0) REVERT: B 121 ASN cc_start: 0.7042 (m-40) cc_final: 0.6782 (t0) REVERT: B 196 SER cc_start: 0.9012 (p) cc_final: 0.8597 (m) REVERT: B 340 LYS cc_start: 0.7411 (tttp) cc_final: 0.7161 (tttt) REVERT: B 344 ASN cc_start: 0.8117 (m-40) cc_final: 0.7904 (m-40) REVERT: B 352 LEU cc_start: 0.8552 (mt) cc_final: 0.8332 (mp) 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: 0.6917 (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: 0.7483 (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: 0.3564 (m-80) REVERT: C 105 ILE cc_start: 0.7899 (mt) cc_final: 0.7638 (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: 0.7804 (m-40) REVERT: C 380 TYR cc_start: 0.7016 (m-80) cc_final: 0.6451 (m-80) REVERT: C 392 ARG cc_start: 0.7745 (ptt90) cc_final: 0.7532 (ppt170) REVERT: C 408 LYS cc_start: 0.6845 (tttp) cc_final: 0.6470 (tptp) REVERT: C 498 SER cc_start: 0.8021 (t) cc_final: 0.7589 (p) REVERT: C 674 GLN cc_start: 0.4243 (mp10) cc_final: 0.3614 (mt0) 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: 0.3935 time to fit residues: 293.5574 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 : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 283 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 693 ASN A 994 GLN B 198 HIS B 587 ASN B 693 ASN B 701 ASN B 748 ASN B 994 GLN B1058 ASN C 121 ASN C 587 ASN C 693 ASN C 701 ASN C 748 ASN C 897 GLN C 994 GLN C1058 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118655 restraints weight = 39335.684| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.24 r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25599 Z= 0.142 Angle : 0.624 8.058 34716 Z= 0.338 Chirality : 0.046 0.216 4113 Planarity : 0.005 0.048 4239 Dihedral : 5.333 45.221 4515 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.73 % Rotamer: Outliers : 1.20 % Allowed : 4.80 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3108 helix: 1.89 (0.21), residues: 666 sheet: 1.24 (0.20), residues: 606 loop : -1.16 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.019 0.001 HIS A 137 PHE 0.031 0.002 PHE B 135 TYR 0.024 0.001 TYR B 161 ARG 0.007 0.001 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 1018) hydrogen bonds : angle 6.15192 ( 2802) covalent geometry : bond 0.00302 (25599) covalent geometry : angle 0.62359 (34716) *********************** 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 368 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 SER cc_start: 0.8712 (p) cc_final: 0.8438 (m) REVERT: A 319 LEU cc_start: 0.6678 (mt) cc_final: 0.6358 (tp) REVERT: A 349 TYR cc_start: 0.8187 (m-80) cc_final: 0.7907 (m-80) REVERT: A 380 TYR cc_start: 0.7421 (m-80) cc_final: 0.7113 (m-80) REVERT: A 408 LYS cc_start: 0.7182 (tttp) cc_final: 0.6819 (tptp) REVERT: A 941 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: B 121 ASN cc_start: 0.7136 (m-40) cc_final: 0.6908 (t0) REVERT: B 196 SER cc_start: 0.8792 (p) cc_final: 0.8489 (m) REVERT: B 319 LEU cc_start: 0.6805 (mm) cc_final: 0.6419 (tp) REVERT: B 380 TYR cc_start: 0.7483 (m-80) cc_final: 0.7131 (m-80) REVERT: B 408 LYS cc_start: 0.7134 (tttp) cc_final: 0.6691 (tptp) REVERT: B 568 ILE cc_start: 0.8293 (mm) cc_final: 0.7977 (pt) REVERT: B 891 ASN cc_start: 0.8634 (t0) cc_final: 0.8369 (t0) REVERT: C 105 ILE cc_start: 0.8039 (mt) cc_final: 0.7776 (mm) REVERT: C 125 ASN cc_start: 0.6925 (m-40) cc_final: 0.6664 (m-40) REVERT: C 181 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7484 (mtm-85) REVERT: C 196 SER cc_start: 0.8805 (p) cc_final: 0.8516 (m) REVERT: C 408 LYS cc_start: 0.7266 (tttp) cc_final: 0.6783 (tptp) REVERT: C 674 GLN cc_start: 0.5035 (mp10) cc_final: 0.4763 (pt0) outliers start: 33 outliers final: 20 residues processed: 360 average time/residue: 0.3319 time to fit residues: 191.7642 Evaluate side-chains 272 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU 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 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 33 THR 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 257 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 209 GLN A 315 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 641 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 HIS B 209 GLN B 315 ASN B 393 GLN B 587 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 693 ASN B 701 ASN B1032 HIS C 230 GLN C 315 ASN C 393 GLN C 587 ASN C 600 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 HIS C1118 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.151284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112678 restraints weight = 39107.764| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.35 r_work: 0.3009 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 25599 Z= 0.364 Angle : 0.765 9.588 34716 Z= 0.405 Chirality : 0.053 0.297 4113 Planarity : 0.006 0.050 4239 Dihedral : 6.529 43.263 4515 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 2.40 % Allowed : 6.99 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3108 helix: 1.44 (0.21), residues: 663 sheet: 0.76 (0.20), residues: 612 loop : -1.69 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 870 HIS 0.016 0.002 HIS A 137 PHE 0.030 0.003 PHE B 440 TYR 0.030 0.003 TYR B 405 ARG 0.010 0.001 ARG C 998 Details of bonding type rmsd hydrogen bonds : bond 0.06345 ( 1018) hydrogen bonds : angle 6.24555 ( 2802) covalent geometry : bond 0.00861 (25599) covalent geometry : angle 0.76496 (34716) *********************** 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 323 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5117 (tmm) cc_final: 0.4888 (tpp) REVERT: A 196 SER cc_start: 0.8799 (p) cc_final: 0.8537 (m) REVERT: A 380 TYR cc_start: 0.7445 (m-80) cc_final: 0.7008 (m-80) REVERT: A 393 GLN cc_start: 0.7468 (tt0) cc_final: 0.7228 (tt0) REVERT: A 408 LYS cc_start: 0.7252 (tttp) cc_final: 0.6804 (tptp) REVERT: A 576 PHE cc_start: 0.7797 (p90) cc_final: 0.7474 (p90) REVERT: A 793 PRO cc_start: 0.4938 (Cg_endo) cc_final: 0.4735 (Cg_exo) REVERT: B 168 MET cc_start: 0.4944 (tmm) cc_final: 0.4697 (tpp) REVERT: B 196 SER cc_start: 0.8828 (p) cc_final: 0.8583 (m) REVERT: B 380 TYR cc_start: 0.7390 (m-80) cc_final: 0.6888 (m-80) REVERT: B 408 LYS cc_start: 0.7273 (tttp) cc_final: 0.6834 (tptp) REVERT: B 568 ILE cc_start: 0.8074 (mm) cc_final: 0.7705 (pt) REVERT: B 576 PHE cc_start: 0.7759 (p90) cc_final: 0.7410 (p90) REVERT: C 105 ILE cc_start: 0.8238 (mt) cc_final: 0.7962 (mm) REVERT: C 168 MET cc_start: 0.5238 (tmm) cc_final: 0.4935 (tpp) REVERT: C 183 PHE cc_start: 0.8493 (m-80) cc_final: 0.8236 (m-80) REVERT: C 196 SER cc_start: 0.8837 (p) cc_final: 0.8565 (m) REVERT: C 408 LYS cc_start: 0.7326 (tttp) cc_final: 0.6814 (tptp) REVERT: C 793 PRO cc_start: 0.4979 (Cg_endo) cc_final: 0.4758 (Cg_exo) outliers start: 66 outliers final: 49 residues processed: 312 average time/residue: 0.3437 time to fit residues: 174.9612 Evaluate side-chains 272 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 318 ASN 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 641 ASN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 600 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 194 optimal weight: 0.6980 chunk 237 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 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 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 693 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN B 919 GLN C 140 ASN C 434 ASN C 490 GLN C 587 ASN C 701 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115608 restraints weight = 39366.619| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.27 r_work: 0.3089 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25599 Z= 0.127 Angle : 0.580 7.645 34716 Z= 0.309 Chirality : 0.045 0.207 4113 Planarity : 0.005 0.055 4239 Dihedral : 5.731 41.993 4515 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 1.64 % Allowed : 8.30 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3108 helix: 1.82 (0.21), residues: 672 sheet: 0.80 (0.20), residues: 609 loop : -1.58 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1086 HIS 0.012 0.001 HIS A 137 PHE 0.023 0.002 PHE B 474 TYR 0.024 0.001 TYR A 161 ARG 0.006 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1018) hydrogen bonds : angle 5.71384 ( 2802) covalent geometry : bond 0.00269 (25599) covalent geometry : angle 0.57960 (34716) *********************** 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 303 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7303 (m-80) cc_final: 0.6924 (m-80) REVERT: A 168 MET cc_start: 0.5162 (tmm) cc_final: 0.4939 (tpp) REVERT: A 191 TYR cc_start: 0.6980 (m-10) cc_final: 0.6774 (m-10) REVERT: A 193 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8525 (mmtp) REVERT: A 196 SER cc_start: 0.8720 (p) cc_final: 0.8490 (m) REVERT: A 319 LEU cc_start: 0.7315 (tt) cc_final: 0.7097 (tt) REVERT: A 405 TYR cc_start: 0.6761 (m-80) cc_final: 0.6481 (m-80) REVERT: A 408 LYS cc_start: 0.7226 (tttp) cc_final: 0.6793 (tptp) REVERT: A 576 PHE cc_start: 0.7733 (p90) cc_final: 0.7433 (p90) REVERT: A 715 MET cc_start: 0.8680 (mtp) cc_final: 0.8410 (mtp) REVERT: B 168 MET cc_start: 0.4939 (tmm) cc_final: 0.4620 (tpp) REVERT: B 196 SER cc_start: 0.8737 (p) cc_final: 0.8478 (m) REVERT: B 408 LYS cc_start: 0.7151 (tttp) cc_final: 0.6723 (tptp) REVERT: B 409 LEU cc_start: 0.7712 (mt) cc_final: 0.7385 (mt) REVERT: B 568 ILE cc_start: 0.8057 (mm) cc_final: 0.7742 (pt) REVERT: B 891 ASN cc_start: 0.8406 (t0) cc_final: 0.7882 (t0) REVERT: C 58 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (m-10) REVERT: C 102 ARG cc_start: 0.7014 (mtt90) cc_final: 0.6542 (mtm-85) REVERT: C 168 MET cc_start: 0.5055 (tmm) cc_final: 0.4854 (tpp) REVERT: C 196 SER cc_start: 0.8757 (p) cc_final: 0.8520 (m) REVERT: C 408 LYS cc_start: 0.7295 (tttp) cc_final: 0.6786 (tptp) REVERT: C 448 PHE cc_start: 0.6754 (m-80) cc_final: 0.6102 (m-80) outliers start: 45 outliers final: 30 residues processed: 296 average time/residue: 0.3419 time to fit residues: 164.3384 Evaluate side-chains 269 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 2.905 ------------------------------------------------------------------------------- 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 193 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 788 GLN 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 108 THR Chi-restraints excluded: chain C residue 135 PHE 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 587 ASN Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 180 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116405 restraints weight = 39190.500| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.21 r_work: 0.3112 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3454 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= 0.117 Angle : 0.549 7.608 34716 Z= 0.292 Chirality : 0.043 0.191 4113 Planarity : 0.005 0.058 4239 Dihedral : 5.176 37.379 4515 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.64 % Allowed : 8.77 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3108 helix: 1.93 (0.21), residues: 687 sheet: 0.81 (0.21), residues: 591 loop : -1.46 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1086 HIS 0.011 0.001 HIS A 137 PHE 0.025 0.001 PHE B 474 TYR 0.024 0.001 TYR C 161 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 1018) hydrogen bonds : angle 5.43043 ( 2802) covalent geometry : bond 0.00250 (25599) covalent geometry : angle 0.54903 (34716) *********************** 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 297 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7634 (m-80) cc_final: 0.7331 (m-80) REVERT: A 168 MET cc_start: 0.5223 (tmm) cc_final: 0.4961 (tpp) REVERT: A 319 LEU cc_start: 0.7326 (tt) cc_final: 0.7004 (tt) REVERT: A 345 CYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 405 TYR cc_start: 0.6929 (m-80) cc_final: 0.6512 (m-80) REVERT: A 408 LYS cc_start: 0.7375 (tttp) cc_final: 0.6888 (tptp) REVERT: A 576 PHE cc_start: 0.7827 (p90) cc_final: 0.7572 (p90) REVERT: B 168 MET cc_start: 0.4856 (tmm) cc_final: 0.4570 (tpp) REVERT: B 212 SER cc_start: 0.8489 (m) cc_final: 0.8217 (p) REVERT: B 319 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6260 (tp) REVERT: B 362 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7632 (ptmt) REVERT: B 405 TYR cc_start: 0.6939 (m-80) cc_final: 0.6682 (m-80) REVERT: B 408 LYS cc_start: 0.7309 (tttp) cc_final: 0.6846 (tptp) REVERT: B 409 LEU cc_start: 0.7671 (mt) cc_final: 0.7351 (mt) REVERT: B 493 ARG cc_start: 0.4653 (mtt180) cc_final: 0.4373 (mmt90) REVERT: B 568 ILE cc_start: 0.8106 (mm) cc_final: 0.7776 (pt) REVERT: B 891 ASN cc_start: 0.8518 (t0) cc_final: 0.8089 (t0) REVERT: C 102 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6647 (mtm-85) REVERT: C 362 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7654 (ptmt) REVERT: C 408 LYS cc_start: 0.7403 (tttp) cc_final: 0.6917 (tptp) outliers start: 45 outliers final: 28 residues processed: 289 average time/residue: 0.3614 time to fit residues: 168.4013 Evaluate side-chains 259 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 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 587 ASN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 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 C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 48 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 609 HIS B 209 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN B1082 ASN C 490 GLN C 587 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114091 restraints weight = 39090.078| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.13 r_work: 0.3077 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25599 Z= 0.180 Angle : 0.589 7.580 34716 Z= 0.312 Chirality : 0.045 0.229 4113 Planarity : 0.005 0.061 4239 Dihedral : 5.390 38.640 4515 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.86 % Allowed : 9.06 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3108 helix: 1.75 (0.21), residues: 684 sheet: 0.68 (0.21), residues: 576 loop : -1.61 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 870 HIS 0.009 0.001 HIS A 137 PHE 0.024 0.002 PHE B 576 TYR 0.026 0.002 TYR B 888 ARG 0.007 0.001 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 1018) hydrogen bonds : angle 5.57038 ( 2802) covalent geometry : bond 0.00417 (25599) covalent geometry : angle 0.58853 (34716) *********************** 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 276 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7636 (m-80) cc_final: 0.7383 (m-80) REVERT: A 168 MET cc_start: 0.5334 (tmm) cc_final: 0.5072 (tpp) REVERT: A 319 LEU cc_start: 0.7331 (tt) cc_final: 0.7079 (tt) REVERT: A 345 CYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7855 (p) REVERT: A 362 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7659 (ptmt) REVERT: A 408 LYS cc_start: 0.7517 (tttp) cc_final: 0.6962 (tptp) REVERT: A 576 PHE cc_start: 0.7784 (p90) cc_final: 0.7443 (p90) REVERT: A 587 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7919 (t0) REVERT: B 64 TRP cc_start: 0.7632 (t60) cc_final: 0.7343 (t60) REVERT: B 168 MET cc_start: 0.4858 (tmm) cc_final: 0.4566 (tpp) REVERT: B 212 SER cc_start: 0.8468 (m) cc_final: 0.8168 (p) REVERT: B 319 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6100 (tp) REVERT: B 345 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 362 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7640 (ptmt) REVERT: B 405 TYR cc_start: 0.6868 (m-80) cc_final: 0.6655 (m-80) REVERT: B 408 LYS cc_start: 0.7378 (tttp) cc_final: 0.6890 (tptp) REVERT: B 493 ARG cc_start: 0.4891 (mtt180) cc_final: 0.4529 (mmm-85) REVERT: B 568 ILE cc_start: 0.8109 (mm) cc_final: 0.7742 (pt) REVERT: B 587 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7663 (t160) REVERT: B 617 TRP cc_start: 0.6374 (m100) cc_final: 0.6021 (m100) REVERT: C 58 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: C 102 ARG cc_start: 0.7135 (mtt90) cc_final: 0.6609 (mtm-85) REVERT: C 345 CYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 362 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7712 (ptmt) REVERT: C 408 LYS cc_start: 0.7426 (tttp) cc_final: 0.6981 (tptp) REVERT: C 448 PHE cc_start: 0.6775 (m-80) cc_final: 0.6515 (m-80) outliers start: 51 outliers final: 33 residues processed: 269 average time/residue: 0.3558 time to fit residues: 156.9965 Evaluate side-chains 254 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 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 587 ASN 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 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 736 LEU 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 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 136 optimal weight: 0.0470 chunk 252 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN B1082 ASN B1118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116740 restraints weight = 39290.111| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.22 r_work: 0.3104 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25599 Z= 0.114 Angle : 0.539 7.560 34716 Z= 0.287 Chirality : 0.043 0.178 4113 Planarity : 0.005 0.068 4239 Dihedral : 5.004 35.420 4515 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.67 % Allowed : 9.10 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3108 helix: 1.81 (0.21), residues: 699 sheet: 0.68 (0.21), residues: 570 loop : -1.52 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1086 HIS 0.009 0.001 HIS A 137 PHE 0.033 0.001 PHE B 474 TYR 0.021 0.001 TYR B1051 ARG 0.007 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1018) hydrogen bonds : angle 5.34401 ( 2802) covalent geometry : bond 0.00237 (25599) covalent geometry : angle 0.53874 (34716) *********************** 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 280 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7368 (m-80) cc_final: 0.7144 (m-80) REVERT: A 168 MET cc_start: 0.5351 (tmm) cc_final: 0.5106 (tpp) REVERT: A 319 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6995 (tt) REVERT: A 345 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7819 (p) REVERT: A 362 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7646 (ptmt) REVERT: A 408 LYS cc_start: 0.7400 (tttp) cc_final: 0.6865 (tptp) REVERT: A 576 PHE cc_start: 0.7664 (p90) cc_final: 0.7370 (p90) REVERT: B 64 TRP cc_start: 0.7544 (t60) cc_final: 0.7303 (t60) REVERT: B 168 MET cc_start: 0.4844 (tmm) cc_final: 0.4599 (tpp) REVERT: B 212 SER cc_start: 0.8451 (m) cc_final: 0.8157 (p) REVERT: B 319 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6046 (tp) REVERT: B 345 CYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 362 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7654 (ptmt) REVERT: B 408 LYS cc_start: 0.7298 (tttp) cc_final: 0.6835 (tptp) REVERT: B 493 ARG cc_start: 0.4894 (mtt180) cc_final: 0.4641 (mmt90) REVERT: B 568 ILE cc_start: 0.8077 (mm) cc_final: 0.7735 (pt) REVERT: B 617 TRP cc_start: 0.6305 (m100) cc_final: 0.6096 (m100) REVERT: B 701 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8178 (t0) REVERT: B 891 ASN cc_start: 0.8302 (t0) cc_final: 0.7806 (t0) REVERT: C 58 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: C 102 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6552 (mtm-85) REVERT: C 345 CYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7455 (p) REVERT: C 362 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7812 (ptpp) REVERT: C 408 LYS cc_start: 0.7319 (tttp) cc_final: 0.6912 (tptp) REVERT: C 448 PHE cc_start: 0.6699 (m-80) cc_final: 0.6463 (m-80) outliers start: 46 outliers final: 32 residues processed: 271 average time/residue: 0.3277 time to fit residues: 146.0641 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 736 LEU 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 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9990 chunk 167 optimal weight: 0.0370 chunk 51 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 243 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 701 ASN C 187 ASN C 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118331 restraints weight = 39115.254| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.23 r_work: 0.3131 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25599 Z= 0.101 Angle : 0.519 7.570 34716 Z= 0.277 Chirality : 0.042 0.156 4113 Planarity : 0.004 0.072 4239 Dihedral : 4.633 34.046 4515 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.75 % Allowed : 9.17 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3108 helix: 1.94 (0.21), residues: 699 sheet: 0.66 (0.21), residues: 573 loop : -1.47 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1086 HIS 0.008 0.001 HIS A 137 PHE 0.036 0.001 PHE B 474 TYR 0.024 0.001 TYR B 405 ARG 0.008 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1018) hydrogen bonds : angle 5.17499 ( 2802) covalent geometry : bond 0.00206 (25599) covalent geometry : angle 0.51906 (34716) *********************** 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 287 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5348 (tmm) cc_final: 0.5117 (tpp) REVERT: A 319 LEU cc_start: 0.7172 (tt) cc_final: 0.6788 (tt) REVERT: A 345 CYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7720 (p) REVERT: A 362 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7616 (ptmt) REVERT: A 408 LYS cc_start: 0.7404 (tttp) cc_final: 0.6912 (tptp) REVERT: A 576 PHE cc_start: 0.7678 (p90) cc_final: 0.7404 (p90) REVERT: B 64 TRP cc_start: 0.7533 (t60) cc_final: 0.7331 (t60) REVERT: B 168 MET cc_start: 0.4826 (tmm) cc_final: 0.4587 (tpp) REVERT: B 212 SER cc_start: 0.8410 (m) cc_final: 0.8127 (p) REVERT: B 319 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.5940 (tp) REVERT: B 345 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7678 (p) REVERT: B 362 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7615 (ptmt) REVERT: B 408 LYS cc_start: 0.7160 (tttp) cc_final: 0.6812 (tptp) REVERT: B 493 ARG cc_start: 0.4861 (mtt180) cc_final: 0.4622 (mmt90) REVERT: B 568 ILE cc_start: 0.8125 (mm) cc_final: 0.7788 (pt) REVERT: B 701 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 891 ASN cc_start: 0.8246 (t0) cc_final: 0.7783 (t0) REVERT: C 32 PHE cc_start: 0.7323 (m-80) cc_final: 0.7091 (m-10) REVERT: C 345 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7437 (p) REVERT: C 362 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7658 (ptmt) REVERT: C 408 LYS cc_start: 0.7322 (tttp) cc_final: 0.6923 (tptp) REVERT: C 448 PHE cc_start: 0.6636 (m-80) cc_final: 0.6411 (m-80) outliers start: 48 outliers final: 32 residues processed: 276 average time/residue: 0.3300 time to fit residues: 149.9403 Evaluate side-chains 259 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 267 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 187 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116835 restraints weight = 39194.001| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.19 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25599 Z= 0.112 Angle : 0.520 7.564 34716 Z= 0.277 Chirality : 0.043 0.158 4113 Planarity : 0.004 0.075 4239 Dihedral : 4.542 33.323 4515 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.60 % Allowed : 9.53 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3108 helix: 1.95 (0.21), residues: 699 sheet: 0.62 (0.21), residues: 588 loop : -1.49 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1086 HIS 0.008 0.001 HIS A 137 PHE 0.028 0.001 PHE B 474 TYR 0.022 0.001 TYR B 161 ARG 0.008 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1018) hydrogen bonds : angle 5.13632 ( 2802) covalent geometry : bond 0.00241 (25599) covalent geometry : angle 0.52043 (34716) *********************** 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 270 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5420 (tmm) cc_final: 0.5166 (tpp) REVERT: A 319 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6790 (tt) REVERT: A 345 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 362 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7594 (ptmt) REVERT: A 408 LYS cc_start: 0.7523 (tttp) cc_final: 0.7021 (tptp) REVERT: A 576 PHE cc_start: 0.7819 (p90) cc_final: 0.7503 (p90) REVERT: B 168 MET cc_start: 0.4888 (tmm) cc_final: 0.4615 (tpp) REVERT: B 212 SER cc_start: 0.8450 (m) cc_final: 0.8189 (p) REVERT: B 345 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7493 (p) REVERT: B 362 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7701 (ptmt) REVERT: B 408 LYS cc_start: 0.7346 (tttp) cc_final: 0.6887 (tptp) REVERT: B 493 ARG cc_start: 0.4918 (mtt180) cc_final: 0.4656 (mmt90) REVERT: B 568 ILE cc_start: 0.8107 (mm) cc_final: 0.7745 (pt) REVERT: B 891 ASN cc_start: 0.8433 (t0) cc_final: 0.8003 (t0) REVERT: C 32 PHE cc_start: 0.7468 (m-80) cc_final: 0.7247 (m-10) REVERT: C 320 CYS cc_start: 0.5549 (m) cc_final: 0.4451 (m) REVERT: C 345 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7404 (p) REVERT: C 362 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7718 (ptmt) REVERT: C 408 LYS cc_start: 0.7443 (tttp) cc_final: 0.7090 (tptp) REVERT: C 448 PHE cc_start: 0.6647 (m-80) cc_final: 0.6407 (m-80) REVERT: C 886 MET cc_start: 0.8960 (mmt) cc_final: 0.8674 (mmt) outliers start: 44 outliers final: 33 residues processed: 258 average time/residue: 0.3199 time to fit residues: 135.7544 Evaluate side-chains 255 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 199 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 0.0970 chunk 118 optimal weight: 4.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112917 restraints weight = 39030.477| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.98 r_work: 0.3125 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25599 Z= 0.124 Angle : 0.527 7.534 34716 Z= 0.280 Chirality : 0.043 0.165 4113 Planarity : 0.005 0.078 4239 Dihedral : 4.554 32.493 4515 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.56 % Allowed : 9.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3108 helix: 1.93 (0.21), residues: 699 sheet: 0.70 (0.21), residues: 570 loop : -1.53 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 143 HIS 0.008 0.001 HIS A 137 PHE 0.034 0.002 PHE A 954 TYR 0.019 0.001 TYR B1051 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1018) hydrogen bonds : angle 5.15337 ( 2802) covalent geometry : bond 0.00278 (25599) covalent geometry : angle 0.52715 (34716) ********************** 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 270 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5460 (tmm) cc_final: 0.5202 (tpp) REVERT: A 319 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6910 (tt) REVERT: A 341 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7241 (ttm-80) REVERT: A 345 CYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7601 (p) REVERT: A 362 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7613 (ptmt) REVERT: A 408 LYS cc_start: 0.7534 (tttp) cc_final: 0.7026 (tptp) REVERT: A 576 PHE cc_start: 0.7737 (p90) cc_final: 0.7416 (p90) REVERT: B 168 MET cc_start: 0.4918 (tmm) cc_final: 0.4649 (tpp) REVERT: B 212 SER cc_start: 0.8447 (m) cc_final: 0.8159 (p) REVERT: B 345 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7597 (p) REVERT: B 362 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7713 (ptmt) REVERT: B 408 LYS cc_start: 0.7419 (tttp) cc_final: 0.6927 (tptp) REVERT: B 493 ARG cc_start: 0.4947 (mtt180) cc_final: 0.4691 (mmt90) REVERT: B 568 ILE cc_start: 0.8103 (mm) cc_final: 0.7737 (pt) REVERT: B 891 ASN cc_start: 0.8407 (t0) cc_final: 0.7935 (t0) REVERT: B 1058 ASN cc_start: 0.7320 (t0) cc_final: 0.7106 (t0) REVERT: C 32 PHE cc_start: 0.7466 (m-80) cc_final: 0.7250 (m-10) REVERT: C 135 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: C 320 CYS cc_start: 0.5627 (m) cc_final: 0.4492 (m) REVERT: C 345 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7360 (p) REVERT: C 362 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7707 (ptmt) REVERT: C 408 LYS cc_start: 0.7404 (tttp) cc_final: 0.7064 (tptp) REVERT: C 674 GLN cc_start: 0.4500 (pm20) cc_final: 0.4248 (pm20) REVERT: C 886 MET cc_start: 0.8942 (mmt) cc_final: 0.8656 (mmt) outliers start: 43 outliers final: 32 residues processed: 259 average time/residue: 0.3437 time to fit residues: 146.4556 Evaluate side-chains 259 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 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 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 20.0000 chunk 260 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 235 optimal weight: 0.0020 chunk 195 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112615 restraints weight = 38887.035| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.03 r_work: 0.3103 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25599 Z= 0.129 Angle : 0.532 7.529 34716 Z= 0.282 Chirality : 0.043 0.171 4113 Planarity : 0.005 0.077 4239 Dihedral : 4.572 30.952 4515 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.46 % Allowed : 9.83 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3108 helix: 1.90 (0.21), residues: 699 sheet: 0.80 (0.21), residues: 564 loop : -1.59 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.008 0.001 HIS A 137 PHE 0.026 0.002 PHE B 576 TYR 0.020 0.001 TYR B 161 ARG 0.007 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1018) hydrogen bonds : angle 5.19206 ( 2802) covalent geometry : bond 0.00290 (25599) covalent geometry : angle 0.53208 (34716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13144.97 seconds wall clock time: 228 minutes 48.26 seconds (13728.26 seconds total)