Starting phenix.real_space_refine on Sat Jun 21 18:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu7_29454/06_2025/8fu7_29454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu7_29454/06_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_29454/06_2025/8fu7_29454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu7_29454/06_2025/8fu7_29454.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu7_29454/06_2025/8fu7_29454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu7_29454/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.05, per 1000 atoms: 0.56 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: 5.54 Conformation dependent library (CDL) restraints added in 2.9 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: 3.73 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: 10.83 Time building geometry restraints manager: 6.55 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: 0.08 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.540 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- 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 : 2.468 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: 0.3806 time to fit residues: 283.8289 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 : 2.593 ------------------------------------------------------------------------------- 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 = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118816 restraints weight = 39366.713| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.25 r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 6.15193 ( 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 : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 SER cc_start: 0.8717 (p) cc_final: 0.8446 (m) REVERT: A 319 LEU cc_start: 0.6679 (mt) cc_final: 0.6359 (tp) REVERT: A 349 TYR cc_start: 0.8188 (m-80) cc_final: 0.7909 (m-80) REVERT: A 380 TYR cc_start: 0.7433 (m-80) cc_final: 0.7125 (m-80) REVERT: A 408 LYS cc_start: 0.7179 (tttp) cc_final: 0.6818 (tptp) REVERT: A 941 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: B 121 ASN cc_start: 0.7137 (m-40) cc_final: 0.6910 (t0) REVERT: B 196 SER cc_start: 0.8797 (p) cc_final: 0.8499 (m) REVERT: B 319 LEU cc_start: 0.6807 (mm) cc_final: 0.6421 (tp) REVERT: B 380 TYR cc_start: 0.7493 (m-80) cc_final: 0.7141 (m-80) REVERT: B 408 LYS cc_start: 0.7132 (tttp) cc_final: 0.6691 (tptp) REVERT: B 568 ILE cc_start: 0.8297 (mm) cc_final: 0.7979 (pt) REVERT: B 891 ASN cc_start: 0.8641 (t0) cc_final: 0.8378 (t0) REVERT: C 105 ILE cc_start: 0.8044 (mt) cc_final: 0.7782 (mm) REVERT: C 125 ASN cc_start: 0.6926 (m-40) cc_final: 0.6665 (m-40) REVERT: C 181 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7488 (mtm-85) REVERT: C 196 SER cc_start: 0.8812 (p) cc_final: 0.8526 (m) REVERT: C 408 LYS cc_start: 0.7264 (tttp) cc_final: 0.6784 (tptp) REVERT: C 674 GLN cc_start: 0.5036 (mp10) cc_final: 0.4762 (pt0) outliers start: 33 outliers final: 20 residues processed: 360 average time/residue: 0.3441 time to fit residues: 200.0568 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 : 2.710 ------------------------------------------------------------------------------- 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: 1.9990 chunk 247 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 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 B 639 HIS B 693 ASN ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 HIS C 230 GLN C 315 ASN C 434 ASN C 490 GLN C 587 ASN C 600 ASN C 639 HIS ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1118 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113016 restraints weight = 39063.882| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.29 r_work: 0.3022 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 25599 Z= 0.314 Angle : 0.744 9.457 34716 Z= 0.394 Chirality : 0.051 0.293 4113 Planarity : 0.006 0.050 4239 Dihedral : 6.541 43.623 4515 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.51 % Allowed : 6.84 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.15), residues: 3108 helix: 1.50 (0.21), residues: 663 sheet: 0.80 (0.21), residues: 591 loop : -1.65 (0.13), residues: 1854 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 0.028 0.003 PHE B 440 TYR 0.025 0.003 TYR B 405 ARG 0.009 0.001 ARG C 998 Details of bonding type rmsd hydrogen bonds : bond 0.06175 ( 1018) hydrogen bonds : angle 6.17820 ( 2802) covalent geometry : bond 0.00751 (25599) covalent geometry : angle 0.74410 (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 330 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5200 (tmm) cc_final: 0.4934 (tpp) REVERT: A 196 SER cc_start: 0.8798 (p) cc_final: 0.8534 (m) REVERT: A 380 TYR cc_start: 0.7413 (m-80) cc_final: 0.6931 (m-80) REVERT: A 408 LYS cc_start: 0.7234 (tttp) cc_final: 0.6799 (tptp) REVERT: A 576 PHE cc_start: 0.7794 (p90) cc_final: 0.7504 (p90) REVERT: B 168 MET cc_start: 0.5041 (tmm) cc_final: 0.4707 (tpp) REVERT: B 196 SER cc_start: 0.8856 (p) cc_final: 0.8618 (m) REVERT: B 380 TYR cc_start: 0.7403 (m-80) cc_final: 0.6851 (m-80) REVERT: B 408 LYS cc_start: 0.7292 (tttp) cc_final: 0.6822 (tptp) REVERT: B 568 ILE cc_start: 0.8062 (mm) cc_final: 0.7677 (pt) REVERT: B 576 PHE cc_start: 0.7720 (p90) cc_final: 0.7361 (p90) REVERT: C 105 ILE cc_start: 0.8230 (mt) cc_final: 0.7961 (mm) REVERT: C 168 MET cc_start: 0.5234 (tmm) cc_final: 0.4922 (tpp) REVERT: C 183 PHE cc_start: 0.8499 (m-80) cc_final: 0.8250 (m-80) REVERT: C 196 SER cc_start: 0.8843 (p) cc_final: 0.8607 (m) REVERT: C 408 LYS cc_start: 0.7312 (tttp) cc_final: 0.6791 (tptp) REVERT: C 793 PRO cc_start: 0.4981 (Cg_endo) cc_final: 0.4766 (Cg_exo) outliers start: 69 outliers final: 47 residues processed: 318 average time/residue: 0.3323 time to fit residues: 175.4552 Evaluate side-chains 270 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 866 ILE 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 539 SER Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 629 THR 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 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 788 GLN 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: 0.9980 chunk 237 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 184 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN B 701 ASN C 140 ASN C 587 ASN C 701 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116293 restraints weight = 39346.386| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25599 Z= 0.123 Angle : 0.572 9.094 34716 Z= 0.305 Chirality : 0.044 0.205 4113 Planarity : 0.005 0.055 4239 Dihedral : 5.580 41.615 4515 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 1.53 % Allowed : 8.33 % Favored : 90.14 % 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: -0.39 (0.15), residues: 3108 helix: 1.88 (0.21), residues: 672 sheet: 0.83 (0.20), residues: 606 loop : -1.57 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1086 HIS 0.012 0.001 HIS A 137 PHE 0.022 0.002 PHE B 474 TYR 0.031 0.001 TYR C 405 ARG 0.006 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1018) hydrogen bonds : angle 5.63265 ( 2802) covalent geometry : bond 0.00261 (25599) covalent geometry : angle 0.57217 (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 302 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5193 (tmm) cc_final: 0.4959 (tpp) REVERT: A 191 TYR cc_start: 0.6907 (m-10) cc_final: 0.6661 (m-10) REVERT: A 319 LEU cc_start: 0.7280 (tt) cc_final: 0.7042 (tt) REVERT: A 405 TYR cc_start: 0.6841 (m-80) cc_final: 0.6539 (m-80) REVERT: A 408 LYS cc_start: 0.7296 (tttp) cc_final: 0.6825 (tptp) REVERT: A 576 PHE cc_start: 0.7731 (p90) cc_final: 0.7462 (p90) REVERT: B 168 MET cc_start: 0.4941 (tmm) cc_final: 0.4655 (tpp) REVERT: B 196 SER cc_start: 0.8705 (p) cc_final: 0.8500 (m) REVERT: B 319 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6291 (tp) REVERT: B 362 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7646 (ptmt) REVERT: B 408 LYS cc_start: 0.7164 (tttp) cc_final: 0.6732 (tptp) REVERT: B 409 LEU cc_start: 0.7682 (mt) cc_final: 0.7331 (mt) REVERT: B 493 ARG cc_start: 0.5162 (mtp85) cc_final: 0.4740 (mmm-85) REVERT: B 568 ILE cc_start: 0.8077 (mm) cc_final: 0.7748 (pt) REVERT: B 891 ASN cc_start: 0.8416 (t0) cc_final: 0.7888 (t0) REVERT: C 58 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: C 196 SER cc_start: 0.8736 (p) cc_final: 0.8517 (m) REVERT: C 408 LYS cc_start: 0.7306 (tttp) cc_final: 0.6810 (tptp) REVERT: C 448 PHE cc_start: 0.6723 (m-80) cc_final: 0.6484 (m-80) outliers start: 42 outliers final: 29 residues processed: 295 average time/residue: 0.3843 time to fit residues: 189.7174 Evaluate side-chains 275 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 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 286 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1034 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 230 GLN ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 639 HIS B 209 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113182 restraints weight = 39224.843| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.20 r_work: 0.3044 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 25599 Z= 0.243 Angle : 0.652 9.064 34716 Z= 0.344 Chirality : 0.047 0.221 4113 Planarity : 0.005 0.056 4239 Dihedral : 6.025 45.202 4515 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.11 % Allowed : 9.06 % Favored : 88.83 % 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: -0.70 (0.15), residues: 3108 helix: 1.69 (0.21), residues: 663 sheet: 0.59 (0.21), residues: 564 loop : -1.72 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 870 HIS 0.010 0.001 HIS A 137 PHE 0.034 0.002 PHE B 474 TYR 0.021 0.002 TYR B1051 ARG 0.007 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1018) hydrogen bonds : angle 5.83857 ( 2802) covalent geometry : bond 0.00579 (25599) covalent geometry : angle 0.65229 (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 283 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5234 (tmm) cc_final: 0.4990 (tpp) REVERT: A 345 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 405 TYR cc_start: 0.6618 (m-80) cc_final: 0.6287 (m-80) REVERT: A 408 LYS cc_start: 0.7457 (tttp) cc_final: 0.6901 (tptp) REVERT: A 576 PHE cc_start: 0.7663 (p90) cc_final: 0.7354 (p90) REVERT: B 64 TRP cc_start: 0.7622 (t60) cc_final: 0.7326 (t60) REVERT: B 168 MET cc_start: 0.4872 (tmm) cc_final: 0.4598 (tpp) REVERT: B 183 PHE cc_start: 0.8423 (m-80) cc_final: 0.8217 (m-80) REVERT: B 212 SER cc_start: 0.8460 (m) cc_final: 0.8158 (p) REVERT: B 345 CYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 362 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7657 (ptmt) REVERT: B 408 LYS cc_start: 0.7339 (tttp) cc_final: 0.6916 (tptp) REVERT: B 493 ARG cc_start: 0.5241 (mtp85) cc_final: 0.5041 (mtt180) REVERT: B 568 ILE cc_start: 0.8083 (mm) cc_final: 0.7683 (pt) REVERT: C 58 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: C 345 CYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7585 (p) REVERT: C 408 LYS cc_start: 0.7375 (tttp) cc_final: 0.6886 (tptp) outliers start: 58 outliers final: 41 residues processed: 277 average time/residue: 0.3282 time to fit residues: 149.2635 Evaluate side-chains 257 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 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 108 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 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 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 B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR 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: 0.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN C 701 ASN C1082 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114762 restraints weight = 39096.354| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.17 r_work: 0.3075 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25599 Z= 0.155 Angle : 0.578 9.141 34716 Z= 0.307 Chirality : 0.044 0.185 4113 Planarity : 0.005 0.062 4239 Dihedral : 5.582 43.712 4515 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.00 % Allowed : 9.50 % Favored : 88.50 % 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: -0.67 (0.15), residues: 3108 helix: 1.68 (0.21), residues: 684 sheet: 0.62 (0.21), residues: 576 loop : -1.75 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1086 HIS 0.009 0.001 HIS A 137 PHE 0.023 0.002 PHE B 474 TYR 0.027 0.001 TYR A 888 ARG 0.008 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 1018) hydrogen bonds : angle 5.57471 ( 2802) covalent geometry : bond 0.00356 (25599) covalent geometry : angle 0.57781 (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 283 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.5355 (tmm) cc_final: 0.5084 (tpp) REVERT: A 319 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.7022 (tt) REVERT: A 345 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 362 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7630 (ptmt) REVERT: A 408 LYS cc_start: 0.7520 (tttp) cc_final: 0.6964 (tptp) REVERT: A 576 PHE cc_start: 0.7745 (p90) cc_final: 0.7410 (p90) REVERT: B 64 TRP cc_start: 0.7565 (t60) cc_final: 0.7288 (t60) REVERT: B 168 MET cc_start: 0.4767 (tmm) cc_final: 0.4486 (tpp) REVERT: B 212 SER cc_start: 0.8491 (m) cc_final: 0.8203 (p) REVERT: B 319 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6063 (tp) REVERT: B 345 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 362 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7716 (ptmt) REVERT: B 408 LYS cc_start: 0.7432 (tttp) cc_final: 0.6965 (tptp) REVERT: B 493 ARG cc_start: 0.5416 (mtp85) cc_final: 0.4981 (mmm-85) REVERT: B 549 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7623 (p90) REVERT: B 568 ILE cc_start: 0.8117 (mm) cc_final: 0.7692 (pt) REVERT: B 617 TRP cc_start: 0.6438 (m100) cc_final: 0.6188 (m100) REVERT: C 345 CYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7541 (p) REVERT: C 362 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7733 (ptmt) REVERT: C 408 LYS cc_start: 0.7438 (tttp) cc_final: 0.6979 (tptp) REVERT: C 448 PHE cc_start: 0.6747 (m-80) cc_final: 0.6512 (m-80) outliers start: 55 outliers final: 36 residues processed: 274 average time/residue: 0.3366 time to fit residues: 152.3280 Evaluate side-chains 261 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 2.857 ------------------------------------------------------------------------------- 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 310 ILE Chi-restraints excluded: chain A residue 318 ASN 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 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 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 549 PHE 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 788 GLN 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 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 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 195 optimal weight: 0.6980 chunk 283 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN C 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116424 restraints weight = 39329.998| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.20 r_work: 0.3099 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25599 Z= 0.121 Angle : 0.544 8.946 34716 Z= 0.289 Chirality : 0.043 0.176 4113 Planarity : 0.005 0.068 4239 Dihedral : 5.078 37.666 4515 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.00 % Allowed : 9.53 % Favored : 88.46 % 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: -0.56 (0.15), residues: 3108 helix: 1.75 (0.21), residues: 702 sheet: 0.63 (0.21), residues: 576 loop : -1.68 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1086 HIS 0.008 0.001 HIS A 137 PHE 0.020 0.001 PHE A 92 TYR 0.021 0.001 TYR B 161 ARG 0.007 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 1018) hydrogen bonds : angle 5.33931 ( 2802) covalent geometry : bond 0.00264 (25599) covalent geometry : angle 0.54388 (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 284 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 2.949 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.5353 (tmm) cc_final: 0.5122 (tpp) REVERT: A 319 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6902 (tt) REVERT: A 345 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7716 (p) REVERT: A 362 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7633 (ptmt) REVERT: A 408 LYS cc_start: 0.7454 (tttp) cc_final: 0.6926 (tptp) REVERT: A 576 PHE cc_start: 0.7610 (p90) cc_final: 0.7313 (p90) REVERT: A 617 TRP cc_start: 0.5479 (t-100) cc_final: 0.5275 (t-100) REVERT: A 919 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 64 TRP cc_start: 0.7497 (t60) cc_final: 0.7275 (t60) REVERT: B 168 MET cc_start: 0.4741 (tmm) cc_final: 0.4505 (tpp) REVERT: B 212 SER cc_start: 0.8431 (m) cc_final: 0.8161 (p) REVERT: B 319 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.5927 (tp) REVERT: B 345 CYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (p) REVERT: B 362 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7677 (ptmt) REVERT: B 405 TYR cc_start: 0.6623 (m-80) cc_final: 0.6311 (m-80) REVERT: B 408 LYS cc_start: 0.7395 (tttp) cc_final: 0.6917 (tptp) REVERT: B 568 ILE cc_start: 0.8137 (mm) cc_final: 0.7747 (pt) REVERT: B 891 ASN cc_start: 0.8363 (t0) cc_final: 0.7829 (t0) REVERT: C 32 PHE cc_start: 0.7280 (m-80) cc_final: 0.7050 (m-10) REVERT: C 345 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7439 (p) REVERT: C 362 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7663 (ptmt) REVERT: C 408 LYS cc_start: 0.7391 (tttp) cc_final: 0.7036 (tptp) REVERT: C 448 PHE cc_start: 0.6759 (m-80) cc_final: 0.6534 (m-80) outliers start: 55 outliers final: 34 residues processed: 273 average time/residue: 0.3156 time to fit residues: 143.6548 Evaluate side-chains 258 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN 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 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9980 chunk 167 optimal weight: 0.0770 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 0.0070 chunk 299 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B1082 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117732 restraints weight = 39129.242| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.24 r_work: 0.3114 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25599 Z= 0.105 Angle : 0.526 9.032 34716 Z= 0.279 Chirality : 0.043 0.224 4113 Planarity : 0.005 0.072 4239 Dihedral : 4.726 33.866 4515 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.60 % Allowed : 9.86 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.15), residues: 3108 helix: 1.90 (0.21), residues: 699 sheet: 0.62 (0.21), residues: 570 loop : -1.61 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1086 HIS 0.008 0.001 HIS A 137 PHE 0.022 0.001 PHE B 448 TYR 0.021 0.001 TYR B1051 ARG 0.008 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1018) hydrogen bonds : angle 5.16920 ( 2802) covalent geometry : bond 0.00219 (25599) covalent geometry : angle 0.52612 (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 273 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 2.742 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.5381 (tmm) cc_final: 0.5163 (tpp) REVERT: A 319 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6663 (tt) REVERT: A 341 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7195 (ttm-80) REVERT: A 345 CYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7678 (p) REVERT: A 362 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7644 (ptmt) REVERT: A 408 LYS cc_start: 0.7477 (tttp) cc_final: 0.6930 (tptp) REVERT: A 576 PHE cc_start: 0.7646 (p90) cc_final: 0.7330 (p90) REVERT: A 617 TRP cc_start: 0.5494 (t-100) cc_final: 0.5246 (t-100) REVERT: B 64 TRP cc_start: 0.7540 (t60) cc_final: 0.7305 (t60) REVERT: B 168 MET cc_start: 0.4772 (tmm) cc_final: 0.4534 (tpp) REVERT: B 212 SER cc_start: 0.8374 (m) cc_final: 0.8123 (p) REVERT: B 319 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.5849 (tp) REVERT: B 345 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7600 (p) REVERT: B 362 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7709 (ptmt) REVERT: B 408 LYS cc_start: 0.7379 (tttp) cc_final: 0.6910 (tptp) REVERT: B 493 ARG cc_start: 0.5311 (mtm180) cc_final: 0.5096 (mmm-85) REVERT: B 568 ILE cc_start: 0.8128 (mm) cc_final: 0.7753 (pt) REVERT: B 891 ASN cc_start: 0.8319 (t0) cc_final: 0.7845 (t0) REVERT: C 345 CYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 362 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7636 (ptmt) REVERT: C 408 LYS cc_start: 0.7399 (tttp) cc_final: 0.6998 (tptp) REVERT: C 448 PHE cc_start: 0.6736 (m-80) cc_final: 0.6522 (m-80) REVERT: C 674 GLN cc_start: 0.4342 (pm20) cc_final: 0.4111 (pm20) REVERT: C 886 MET cc_start: 0.8870 (mmt) cc_final: 0.8526 (mmt) outliers start: 44 outliers final: 35 residues processed: 260 average time/residue: 0.3312 time to fit residues: 142.3722 Evaluate side-chains 258 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN 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 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 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 617 TRP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114660 restraints weight = 39159.741| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.19 r_work: 0.3074 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4074 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 : 0.580 9.324 34716 Z= 0.306 Chirality : 0.044 0.186 4113 Planarity : 0.005 0.074 4239 Dihedral : 5.058 33.193 4515 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.75 % Allowed : 9.83 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.15), residues: 3108 helix: 1.68 (0.20), residues: 702 sheet: 0.63 (0.21), residues: 573 loop : -1.74 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 870 HIS 0.008 0.001 HIS A 137 PHE 0.028 0.002 PHE B 576 TYR 0.023 0.002 TYR B 161 ARG 0.007 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 1018) hydrogen bonds : angle 5.41949 ( 2802) covalent geometry : bond 0.00422 (25599) covalent geometry : angle 0.57953 (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 265 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.5446 (tmm) cc_final: 0.5197 (tpp) REVERT: A 345 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7615 (p) REVERT: A 362 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7574 (ptmt) REVERT: A 408 LYS cc_start: 0.7612 (tttp) cc_final: 0.7043 (tptp) REVERT: A 576 PHE cc_start: 0.7777 (p90) cc_final: 0.7424 (p90) REVERT: A 617 TRP cc_start: 0.5731 (t-100) cc_final: 0.5147 (t-100) REVERT: B 168 MET cc_start: 0.4827 (tmm) cc_final: 0.4563 (tpp) REVERT: B 212 SER cc_start: 0.8379 (m) cc_final: 0.8126 (p) REVERT: B 319 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.5834 (tp) REVERT: B 345 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 362 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7707 (ptmt) REVERT: B 405 TYR cc_start: 0.6875 (m-80) cc_final: 0.6460 (m-80) REVERT: B 408 LYS cc_start: 0.7571 (tttp) cc_final: 0.7049 (tptp) REVERT: B 493 ARG cc_start: 0.5372 (mtm180) cc_final: 0.5095 (mtt180) REVERT: C 320 CYS cc_start: 0.5612 (m) cc_final: 0.4714 (m) REVERT: C 345 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7693 (p) REVERT: C 362 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7668 (ptmt) REVERT: C 408 LYS cc_start: 0.7531 (tttp) cc_final: 0.7179 (tptp) outliers start: 48 outliers final: 36 residues processed: 255 average time/residue: 0.3488 time to fit residues: 147.4208 Evaluate side-chains 249 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 369 THR 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 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 286 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.153676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114948 restraints weight = 39005.250| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.17 r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25599 Z= 0.155 Angle : 0.560 9.463 34716 Z= 0.297 Chirality : 0.044 0.192 4113 Planarity : 0.005 0.078 4239 Dihedral : 5.022 32.894 4515 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.64 % Allowed : 10.04 % Favored : 88.32 % 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: -0.64 (0.15), residues: 3108 helix: 1.68 (0.20), residues: 702 sheet: 0.64 (0.21), residues: 573 loop : -1.75 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.008 0.001 HIS A 137 PHE 0.028 0.002 PHE B 576 TYR 0.021 0.001 TYR A 888 ARG 0.008 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 1018) hydrogen bonds : angle 5.38080 ( 2802) covalent geometry : bond 0.00360 (25599) covalent geometry : angle 0.56034 (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 259 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 2.847 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.3086 (ttt) cc_final: 0.2761 (tmm) REVERT: A 168 MET cc_start: 0.5414 (tmm) cc_final: 0.5184 (tpp) REVERT: A 345 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 362 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7640 (ptmt) REVERT: A 408 LYS cc_start: 0.7530 (tttp) cc_final: 0.6971 (tptp) REVERT: A 576 PHE cc_start: 0.7661 (p90) cc_final: 0.7325 (p90) REVERT: A 617 TRP cc_start: 0.5684 (t-100) cc_final: 0.5262 (t-100) REVERT: B 168 MET cc_start: 0.4862 (tmm) cc_final: 0.4627 (tpp) REVERT: B 212 SER cc_start: 0.8344 (m) cc_final: 0.8098 (p) REVERT: B 345 CYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 362 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7674 (ptmt) REVERT: B 408 LYS cc_start: 0.7459 (tttp) cc_final: 0.6942 (tptp) REVERT: B 493 ARG cc_start: 0.5379 (mtm180) cc_final: 0.5172 (mmm-85) REVERT: B 891 ASN cc_start: 0.8322 (t0) cc_final: 0.7943 (t0) REVERT: C 320 CYS cc_start: 0.5565 (m) cc_final: 0.4923 (m) REVERT: C 362 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7632 (ptmt) REVERT: C 408 LYS cc_start: 0.7450 (tttp) cc_final: 0.7112 (tptp) REVERT: C 448 PHE cc_start: 0.6727 (m-80) cc_final: 0.6464 (m-80) outliers start: 45 outliers final: 35 residues processed: 249 average time/residue: 0.3462 time to fit residues: 144.5117 Evaluate side-chains 247 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 2.908 ------------------------------------------------------------------------------- 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 286 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR 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 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR 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 1034 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL 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 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 5.9990 chunk 260 optimal weight: 0.0000 chunk 230 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 318 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.154710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116104 restraints weight = 38877.333| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.14 r_work: 0.3118 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25599 Z= 0.111 Angle : 0.530 9.372 34716 Z= 0.282 Chirality : 0.043 0.179 4113 Planarity : 0.005 0.078 4239 Dihedral : 4.718 32.048 4515 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.38 % Allowed : 10.30 % Favored : 88.32 % 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: -0.53 (0.15), residues: 3108 helix: 1.85 (0.21), residues: 699 sheet: 0.62 (0.21), residues: 576 loop : -1.67 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.008 0.001 HIS A 137 PHE 0.026 0.001 PHE B 576 TYR 0.024 0.001 TYR B 161 ARG 0.008 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 1018) hydrogen bonds : angle 5.20641 ( 2802) covalent geometry : bond 0.00238 (25599) covalent geometry : angle 0.52994 (34716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13570.72 seconds wall clock time: 236 minutes 28.37 seconds (14188.37 seconds total)