Starting phenix.real_space_refine on Thu Mar 5 14:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyz_32899/03_2026/7wyz_32899.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 26 5.49 5 Mg 2 5.21 5 S 118 5.16 5 Na 4 4.78 5 C 14690 2.51 5 N 3514 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22682 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 516 Unusual residues: {' MG': 1, ' NA': 2, 'CLR': 1, 'OBN': 1, 'PCW': 10} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'CLR': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D, E, K, L, M, N Time building chain proxies: 9.27, per 1000 atoms: 0.41 Number of scatterers: 22682 At special positions: 0 Unit cell: (216.276, 179.692, 104.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 118 16.00 P 26 15.00 Mg 2 11.99 Na 4 11.00 O 4328 8.00 N 3514 7.00 C 14690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 691.5 milliseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 49.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.636A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.590A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.697A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.977A pdb=" N VAL A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.661A pdb=" N SER A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.803A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.676A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.655A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.292A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.555A pdb=" N ILE A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.650A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.508A pdb=" N LEU A 883 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 884' Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 4.034A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.561A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.760A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.553A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 29 through 62 removed outlier: 3.817A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.518A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.818A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.334A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.746A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.184A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.635A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 313 Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.590A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.697A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.977A pdb=" N VAL C 364 " --> pdb=" O LEU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.662A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.803A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.676A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 707 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.656A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 755 through 782 removed outlier: 4.291A pdb=" N VAL C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 786 Processing helix chain 'C' and resid 787 through 797 Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.555A pdb=" N ILE C 807 " --> pdb=" O GLY C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.651A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 3.509A pdb=" N LEU C 883 " --> pdb=" O LEU C 879 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 879 through 884' Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 4.034A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.562A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.760A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.554A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1022 Processing helix chain 'D' and resid 29 through 62 removed outlier: 3.817A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.517A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.818A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.334A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.746A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.183A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.795A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226 removed outlier: 4.156A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.692A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.871A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.543A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.121A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.796A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.155A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.691A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.871A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.543A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.122A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AB9, first strand: chain 'D' and resid 78 through 80 Processing sheet with id=AC1, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AC2, first strand: chain 'D' and resid 124 through 125 1010 hydrogen bonds defined for protein. 2922 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: 4.46 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6686 1.34 - 1.46: 4405 1.46 - 1.58: 11785 1.58 - 1.70: 68 1.70 - 1.82: 172 Bond restraints: 23116 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.506 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.507 0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C39 PCW C1113 " pdb=" C40 PCW C1113 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C19 PCW C1109 " pdb=" C20 PCW C1109 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C19 PCW A1109 " pdb=" C20 PCW A1109 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 23111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 29249 2.37 - 4.74: 1509 4.74 - 7.11: 311 7.11 - 9.47: 102 9.47 - 11.84: 39 Bond angle restraints: 31210 Sorted by residual: angle pdb=" N GLY A 855 " pdb=" CA GLY A 855 " pdb=" C GLY A 855 " ideal model delta sigma weight residual 113.18 123.43 -10.25 2.37e+00 1.78e-01 1.87e+01 angle pdb=" N GLY C 855 " pdb=" CA GLY C 855 " pdb=" C GLY C 855 " ideal model delta sigma weight residual 113.18 123.37 -10.19 2.37e+00 1.78e-01 1.85e+01 angle pdb=" CA TYR C 488 " pdb=" CB TYR C 488 " pdb=" CG TYR C 488 " ideal model delta sigma weight residual 113.90 121.35 -7.45 1.80e+00 3.09e-01 1.71e+01 angle pdb=" CA TYR A 488 " pdb=" CB TYR A 488 " pdb=" CG TYR A 488 " ideal model delta sigma weight residual 113.90 121.33 -7.43 1.80e+00 3.09e-01 1.70e+01 angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 ... (remaining 31205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 14294 35.97 - 71.93: 752 71.93 - 107.90: 80 107.90 - 143.87: 40 143.87 - 179.83: 2 Dihedral angle restraints: 15168 sinusoidal: 7512 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E1303 " pdb=" C31 PCW E1303 " pdb=" C32 PCW E1303 " pdb=" O2 PCW E1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.66 -179.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G1303 " pdb=" C31 PCW G1303 " pdb=" C32 PCW G1303 " pdb=" O2 PCW G1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.63 -179.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW C1112 " pdb=" C31 PCW C1112 " pdb=" C32 PCW C1112 " pdb=" O2 PCW C1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.59 -138.58 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2848 0.068 - 0.136: 554 0.136 - 0.203: 88 0.203 - 0.271: 22 0.271 - 0.339: 30 Chirality restraints: 3542 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.92e+01 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.90e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.10e+01 ... (remaining 3539 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.079 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO D 123 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.079 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO B 123 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO A 125 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.046 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 16242 3.11 - 3.71: 31455 3.71 - 4.30: 47348 4.30 - 4.90: 77377 Nonbonded interactions: 172522 Sorted by model distance: nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.914 2.170 nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.915 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A2001 " model vdw 1.956 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C2001 " model vdw 1.961 2.170 nonbonded pdb=" O THR C 378 " pdb="MG MG C1101 " model vdw 2.027 2.170 ... (remaining 172517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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: 0.910 Set stop_for_unknowns flag: 0.010 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.011 0.310 23160 Z= 0.538 Angle : 1.310 16.857 31336 Z= 0.587 Chirality : 0.063 0.339 3542 Planarity : 0.008 0.123 3806 Dihedral : 19.894 179.834 10238 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.89 % Favored : 91.65 % Rotamer: Outliers : 10.39 % Allowed : 8.18 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.14), residues: 2636 helix: -1.43 (0.13), residues: 1202 sheet: -2.39 (0.28), residues: 252 loop : -2.69 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 596 TYR 0.043 0.002 TYR B 40 PHE 0.022 0.002 PHE D 297 TRP 0.022 0.002 TRP C 894 HIS 0.008 0.002 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.01084 (23116) covalent geometry : angle 1.28883 (31210) SS BOND : bond 0.00168 ( 6) SS BOND : angle 1.74507 ( 12) hydrogen bonds : bond 0.16253 ( 1010) hydrogen bonds : angle 7.00254 ( 2922) link_ALPHA1-3 : bond 0.00723 ( 6) link_ALPHA1-3 : angle 3.00120 ( 18) link_ALPHA1-6 : bond 0.00638 ( 4) link_ALPHA1-6 : angle 1.32189 ( 12) link_BETA1-2 : bond 0.00564 ( 2) link_BETA1-2 : angle 5.49930 ( 6) link_BETA1-4 : bond 0.00782 ( 14) link_BETA1-4 : angle 5.60985 ( 42) link_BETA1-6 : bond 0.00276 ( 4) link_BETA1-6 : angle 0.81941 ( 12) link_NAG-ASN : bond 0.01072 ( 8) link_NAG-ASN : angle 2.85553 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 509 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6905 (mttt) REVERT: A 65 ASN cc_start: 0.6580 (OUTLIER) cc_final: 0.6145 (t0) REVERT: A 100 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 127 ASN cc_start: 0.6378 (OUTLIER) cc_final: 0.4816 (t0) REVERT: A 267 MET cc_start: 0.8567 (ppp) cc_final: 0.8188 (ppp) REVERT: A 331 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: A 381 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8677 (mt) REVERT: A 411 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6816 (p90) REVERT: A 493 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6280 (m90) REVERT: A 692 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7192 (tpt170) REVERT: A 747 ASP cc_start: 0.7882 (m-30) cc_final: 0.7665 (m-30) REVERT: A 795 ILE cc_start: 0.8876 (mm) cc_final: 0.8582 (mt) REVERT: A 846 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7866 (p0) REVERT: A 949 MET cc_start: 0.8476 (mmm) cc_final: 0.8207 (mtp) REVERT: B 20 SER cc_start: 0.6290 (OUTLIER) cc_final: 0.5379 (p) REVERT: B 195 THR cc_start: 0.7972 (m) cc_final: 0.7695 (p) REVERT: B 203 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6419 (mm-40) REVERT: G 11 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8228 (ttt180) REVERT: C 37 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6992 (mttt) REVERT: C 65 ASN cc_start: 0.6350 (OUTLIER) cc_final: 0.5881 (t0) REVERT: C 100 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: C 127 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.5298 (t0) REVERT: C 231 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7457 (t80) REVERT: C 260 TYR cc_start: 0.6949 (m-80) cc_final: 0.6637 (m-10) REVERT: C 267 MET cc_start: 0.8358 (ppp) cc_final: 0.8107 (ppp) REVERT: C 331 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8238 (m-40) REVERT: C 381 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 411 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6762 (p90) REVERT: C 493 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6556 (m90) REVERT: C 515 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7325 (pp) REVERT: C 747 ASP cc_start: 0.8085 (m-30) cc_final: 0.7884 (m-30) REVERT: C 825 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 1007 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (t80) REVERT: D 20 SER cc_start: 0.6198 (OUTLIER) cc_final: 0.5310 (p) REVERT: D 106 MET cc_start: 0.8691 (mmm) cc_final: 0.8172 (mmm) REVERT: D 168 TYR cc_start: 0.7717 (m-80) cc_final: 0.7210 (m-80) REVERT: D 195 THR cc_start: 0.7953 (m) cc_final: 0.7606 (p) REVERT: E 11 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8321 (ttt180) outliers start: 235 outliers final: 39 residues processed: 677 average time/residue: 0.1856 time to fit residues: 182.9410 Evaluate side-chains 303 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 241 ASN A 434 GLN A 474 ASN A 539 GLN A 620 HIS A 744 GLN A 904 GLN A1019 GLN B 56 GLN B 203 GLN B 258 GLN C 129 ASN C 474 ASN C 744 GLN C 904 GLN C1019 GLN D 56 GLN D 107 HIS D 146 GLN D 243 GLN D 258 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095679 restraints weight = 34543.894| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.18 r_work: 0.2959 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23160 Z= 0.158 Angle : 0.701 10.828 31336 Z= 0.332 Chirality : 0.047 0.421 3542 Planarity : 0.005 0.054 3806 Dihedral : 16.822 179.797 5408 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.63 % Allowed : 12.25 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.16), residues: 2636 helix: 0.54 (0.15), residues: 1196 sheet: -1.87 (0.28), residues: 248 loop : -1.83 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 517 TYR 0.020 0.001 TYR D 40 PHE 0.019 0.002 PHE C 793 TRP 0.016 0.001 TRP C 317 HIS 0.009 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00344 (23116) covalent geometry : angle 0.67335 (31210) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.91526 ( 12) hydrogen bonds : bond 0.05960 ( 1010) hydrogen bonds : angle 4.87670 ( 2922) link_ALPHA1-3 : bond 0.01074 ( 6) link_ALPHA1-3 : angle 3.98289 ( 18) link_ALPHA1-6 : bond 0.00799 ( 4) link_ALPHA1-6 : angle 2.30694 ( 12) link_BETA1-2 : bond 0.00277 ( 2) link_BETA1-2 : angle 4.85071 ( 6) link_BETA1-4 : bond 0.00648 ( 14) link_BETA1-4 : angle 3.81995 ( 42) link_BETA1-6 : bond 0.01182 ( 4) link_BETA1-6 : angle 1.48504 ( 12) link_NAG-ASN : bond 0.00628 ( 8) link_NAG-ASN : angle 2.31162 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 262 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7505 (pt0) REVERT: A 65 ASN cc_start: 0.7018 (m-40) cc_final: 0.6464 (t0) REVERT: A 100 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 127 ASN cc_start: 0.6235 (OUTLIER) cc_final: 0.4737 (t0) REVERT: A 331 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: A 434 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6412 (mm110) REVERT: A 489 GLN cc_start: 0.6451 (tt0) cc_final: 0.6157 (tt0) REVERT: A 493 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.6109 (m90) REVERT: A 512 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 558 PHE cc_start: 0.6195 (t80) cc_final: 0.5856 (t80) REVERT: A 737 SER cc_start: 0.8565 (m) cc_final: 0.8315 (p) REVERT: B 13 TRP cc_start: 0.5472 (t60) cc_final: 0.5211 (t-100) REVERT: B 20 SER cc_start: 0.6532 (OUTLIER) cc_final: 0.5813 (p) REVERT: B 168 TYR cc_start: 0.8679 (m-80) cc_final: 0.8250 (m-80) REVERT: B 286 ASP cc_start: 0.8648 (t0) cc_final: 0.8145 (m-30) REVERT: C 45 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7367 (mttt) REVERT: C 100 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: C 127 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.4991 (t0) REVERT: C 156 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6539 (mtm180) REVERT: C 158 MET cc_start: 0.8052 (tpp) cc_final: 0.7623 (tpp) REVERT: C 231 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7578 (t80) REVERT: C 267 MET cc_start: 0.8791 (ppp) cc_final: 0.8498 (ppp) REVERT: C 331 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8401 (m-40) REVERT: C 430 ARG cc_start: 0.8305 (ptp-110) cc_final: 0.7735 (ttp80) REVERT: C 489 GLN cc_start: 0.6751 (tt0) cc_final: 0.6455 (tt0) REVERT: C 578 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: C 658 ARG cc_start: 0.7322 (mmt-90) cc_final: 0.6837 (mmp-170) REVERT: C 737 SER cc_start: 0.8638 (m) cc_final: 0.8300 (p) REVERT: C 825 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 837 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8666 (ptt-90) REVERT: C 1007 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (t80) REVERT: D 20 SER cc_start: 0.6525 (OUTLIER) cc_final: 0.5842 (p) REVERT: D 106 MET cc_start: 0.9184 (mmm) cc_final: 0.8577 (mmm) REVERT: D 129 ASP cc_start: 0.8426 (t0) cc_final: 0.8179 (t0) REVERT: D 168 TYR cc_start: 0.8508 (m-80) cc_final: 0.7997 (m-80) REVERT: D 180 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8736 (pttt) REVERT: D 237 TYR cc_start: 0.8297 (m-80) cc_final: 0.8001 (m-80) REVERT: E 11 ARG cc_start: 0.8913 (ttm-80) cc_final: 0.8543 (ttt180) outliers start: 82 outliers final: 31 residues processed: 328 average time/residue: 0.1575 time to fit residues: 78.2595 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 239 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 192 optimal weight: 0.0970 chunk 64 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 chunk 236 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100078 restraints weight = 33957.656| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.19 r_work: 0.3050 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23160 Z= 0.110 Angle : 0.583 10.286 31336 Z= 0.272 Chirality : 0.043 0.423 3542 Planarity : 0.004 0.039 3806 Dihedral : 15.590 177.556 5335 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.83 % Allowed : 13.31 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2636 helix: 1.17 (0.15), residues: 1204 sheet: -1.43 (0.29), residues: 268 loop : -1.35 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 255 TYR 0.024 0.001 TYR A 488 PHE 0.017 0.001 PHE A 793 TRP 0.009 0.001 TRP D 156 HIS 0.008 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00222 (23116) covalent geometry : angle 0.55469 (31210) SS BOND : bond 0.00094 ( 6) SS BOND : angle 0.75201 ( 12) hydrogen bonds : bond 0.04796 ( 1010) hydrogen bonds : angle 4.43513 ( 2922) link_ALPHA1-3 : bond 0.01147 ( 6) link_ALPHA1-3 : angle 3.57639 ( 18) link_ALPHA1-6 : bond 0.00767 ( 4) link_ALPHA1-6 : angle 1.77033 ( 12) link_BETA1-2 : bond 0.00469 ( 2) link_BETA1-2 : angle 4.76245 ( 6) link_BETA1-4 : bond 0.00815 ( 14) link_BETA1-4 : angle 3.50032 ( 42) link_BETA1-6 : bond 0.00284 ( 4) link_BETA1-6 : angle 1.42058 ( 12) link_NAG-ASN : bond 0.01069 ( 8) link_NAG-ASN : angle 2.05660 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 245 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7512 (pt0) REVERT: A 65 ASN cc_start: 0.6780 (m-40) cc_final: 0.6400 (t0) REVERT: A 100 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: A 127 ASN cc_start: 0.6281 (OUTLIER) cc_final: 0.4728 (t0) REVERT: A 231 PHE cc_start: 0.7675 (t80) cc_final: 0.7011 (t80) REVERT: A 331 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8441 (m-40) REVERT: A 434 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6420 (mm110) REVERT: A 489 GLN cc_start: 0.6603 (tt0) cc_final: 0.6289 (tt0) REVERT: A 512 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: A 534 MET cc_start: 0.6772 (mpp) cc_final: 0.6544 (mpp) REVERT: A 558 PHE cc_start: 0.6311 (t80) cc_final: 0.6083 (t80) REVERT: A 658 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7172 (mmp80) REVERT: A 1007 PHE cc_start: 0.8690 (t80) cc_final: 0.8392 (t80) REVERT: B 20 SER cc_start: 0.6378 (OUTLIER) cc_final: 0.5686 (p) REVERT: B 73 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 168 TYR cc_start: 0.8655 (m-80) cc_final: 0.8339 (m-80) REVERT: B 286 ASP cc_start: 0.8532 (t0) cc_final: 0.8215 (m-30) REVERT: C 45 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7540 (mttt) REVERT: C 127 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.4994 (t0) REVERT: C 231 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7575 (t80) REVERT: C 255 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8173 (mtt90) REVERT: C 331 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8240 (m-40) REVERT: C 489 GLN cc_start: 0.6746 (tt0) cc_final: 0.6485 (tt0) REVERT: C 512 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: C 578 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: C 658 ARG cc_start: 0.7248 (mmt-90) cc_final: 0.6818 (mmp-170) REVERT: C 737 SER cc_start: 0.8548 (m) cc_final: 0.8329 (p) REVERT: C 872 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8919 (mt) REVERT: D 20 SER cc_start: 0.6333 (OUTLIER) cc_final: 0.5676 (p) REVERT: D 106 MET cc_start: 0.9102 (mmm) cc_final: 0.8510 (mmm) REVERT: D 155 MET cc_start: 0.8588 (mmm) cc_final: 0.8294 (mmt) REVERT: D 168 TYR cc_start: 0.8392 (m-80) cc_final: 0.8014 (m-80) REVERT: D 180 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8788 (pttt) outliers start: 64 outliers final: 31 residues processed: 299 average time/residue: 0.1543 time to fit residues: 71.6792 Evaluate side-chains 252 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 202 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 107 optimal weight: 0.0020 chunk 192 optimal weight: 0.9980 overall best weight: 2.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN B 70 GLN B 243 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.092510 restraints weight = 34010.628| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.26 r_work: 0.2860 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23160 Z= 0.174 Angle : 0.634 9.236 31336 Z= 0.302 Chirality : 0.046 0.468 3542 Planarity : 0.004 0.045 3806 Dihedral : 14.623 177.479 5324 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.14 % Allowed : 14.32 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2636 helix: 1.42 (0.15), residues: 1190 sheet: -0.62 (0.30), residues: 298 loop : -1.07 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.016 0.002 TYR D 40 PHE 0.025 0.002 PHE A 793 TRP 0.035 0.002 TRP A 392 HIS 0.007 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00409 (23116) covalent geometry : angle 0.60952 (31210) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.97211 ( 12) hydrogen bonds : bond 0.06051 ( 1010) hydrogen bonds : angle 4.33442 ( 2922) link_ALPHA1-3 : bond 0.01543 ( 6) link_ALPHA1-3 : angle 4.01876 ( 18) link_ALPHA1-6 : bond 0.00645 ( 4) link_ALPHA1-6 : angle 1.81401 ( 12) link_BETA1-2 : bond 0.00395 ( 2) link_BETA1-2 : angle 4.39247 ( 6) link_BETA1-4 : bond 0.00853 ( 14) link_BETA1-4 : angle 3.34566 ( 42) link_BETA1-6 : bond 0.00441 ( 4) link_BETA1-6 : angle 1.64160 ( 12) link_NAG-ASN : bond 0.00666 ( 8) link_NAG-ASN : angle 1.41250 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 221 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7452 (pt0) REVERT: A 65 ASN cc_start: 0.6503 (m-40) cc_final: 0.6163 (t0) REVERT: A 100 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 127 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.5856 (p0) REVERT: A 231 PHE cc_start: 0.7809 (t80) cc_final: 0.7123 (t80) REVERT: A 331 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8551 (m-40) REVERT: A 434 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6574 (mm110) REVERT: A 534 MET cc_start: 0.7009 (mpp) cc_final: 0.6751 (mpp) REVERT: A 658 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.7124 (mmp-170) REVERT: A 1007 PHE cc_start: 0.8676 (t80) cc_final: 0.8439 (t80) REVERT: B 180 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8939 (pttm) REVERT: B 195 THR cc_start: 0.7922 (m) cc_final: 0.7657 (p) REVERT: B 286 ASP cc_start: 0.8718 (t0) cc_final: 0.8464 (m-30) REVERT: C 33 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: C 45 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7521 (mttt) REVERT: C 100 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: C 158 MET cc_start: 0.8089 (tpp) cc_final: 0.7347 (ttp) REVERT: C 202 ASP cc_start: 0.8011 (m-30) cc_final: 0.7731 (t0) REVERT: C 255 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8095 (mtt90) REVERT: C 331 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8402 (m-40) REVERT: C 487 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7172 (mmmt) REVERT: C 489 GLN cc_start: 0.6784 (tt0) cc_final: 0.6431 (tt0) REVERT: C 558 PHE cc_start: 0.6390 (t80) cc_final: 0.6103 (t80) REVERT: C 578 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5492 (m-80) REVERT: C 658 ARG cc_start: 0.7327 (mmt-90) cc_final: 0.6983 (mmp-170) REVERT: C 737 SER cc_start: 0.8793 (m) cc_final: 0.8587 (p) REVERT: D 106 MET cc_start: 0.9139 (mmm) cc_final: 0.8528 (mmm) REVERT: D 168 TYR cc_start: 0.8913 (m-80) cc_final: 0.8683 (m-80) outliers start: 71 outliers final: 41 residues processed: 282 average time/residue: 0.1574 time to fit residues: 69.2718 Evaluate side-chains 248 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 189 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 234 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN A 904 GLN B 70 GLN B 146 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092739 restraints weight = 33689.533| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.17 r_work: 0.2870 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23160 Z= 0.108 Angle : 0.561 9.218 31336 Z= 0.260 Chirality : 0.043 0.478 3542 Planarity : 0.003 0.037 3806 Dihedral : 13.924 177.643 5318 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 16.18 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2636 helix: 1.67 (0.15), residues: 1206 sheet: -0.33 (0.30), residues: 298 loop : -1.00 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.017 0.001 TYR A 684 PHE 0.023 0.001 PHE A 558 TRP 0.014 0.001 TRP A 392 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00232 (23116) covalent geometry : angle 0.53466 (31210) SS BOND : bond 0.00111 ( 6) SS BOND : angle 1.48560 ( 12) hydrogen bonds : bond 0.04757 ( 1010) hydrogen bonds : angle 4.09367 ( 2922) link_ALPHA1-3 : bond 0.01257 ( 6) link_ALPHA1-3 : angle 3.84327 ( 18) link_ALPHA1-6 : bond 0.00659 ( 4) link_ALPHA1-6 : angle 1.78925 ( 12) link_BETA1-2 : bond 0.00591 ( 2) link_BETA1-2 : angle 4.40461 ( 6) link_BETA1-4 : bond 0.00744 ( 14) link_BETA1-4 : angle 3.15083 ( 42) link_BETA1-6 : bond 0.00166 ( 4) link_BETA1-6 : angle 1.52615 ( 12) link_NAG-ASN : bond 0.00599 ( 8) link_NAG-ASN : angle 1.45273 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7475 (pt0) REVERT: A 65 ASN cc_start: 0.6492 (m-40) cc_final: 0.6129 (t0) REVERT: A 127 ASN cc_start: 0.6282 (OUTLIER) cc_final: 0.5690 (p0) REVERT: A 231 PHE cc_start: 0.7831 (t80) cc_final: 0.7152 (t80) REVERT: A 331 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: A 427 LEU cc_start: 0.8869 (mm) cc_final: 0.8589 (mm) REVERT: A 434 GLN cc_start: 0.7017 (mm-40) cc_final: 0.6682 (mm110) REVERT: A 534 MET cc_start: 0.7055 (mpp) cc_final: 0.6747 (mpp) REVERT: A 558 PHE cc_start: 0.6043 (t80) cc_final: 0.5633 (t80) REVERT: A 1007 PHE cc_start: 0.8625 (t80) cc_final: 0.8395 (t80) REVERT: B 73 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 180 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8755 (ptpt) REVERT: B 195 THR cc_start: 0.7793 (m) cc_final: 0.7566 (p) REVERT: B 237 TYR cc_start: 0.8392 (m-80) cc_final: 0.8042 (m-80) REVERT: B 286 ASP cc_start: 0.8663 (t0) cc_final: 0.8436 (m-30) REVERT: C 45 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7611 (mttt) REVERT: C 100 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: C 127 ASN cc_start: 0.6582 (OUTLIER) cc_final: 0.5121 (t0) REVERT: C 156 ARG cc_start: 0.6732 (mtt180) cc_final: 0.6525 (mtm180) REVERT: C 158 MET cc_start: 0.8084 (tpp) cc_final: 0.7368 (ttp) REVERT: C 202 ASP cc_start: 0.7918 (m-30) cc_final: 0.7626 (t0) REVERT: C 231 PHE cc_start: 0.7882 (t80) cc_final: 0.7194 (t80) REVERT: C 331 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8479 (m-40) REVERT: C 427 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 487 LYS cc_start: 0.7395 (mmtt) cc_final: 0.7189 (mmmt) REVERT: C 489 GLN cc_start: 0.6504 (tt0) cc_final: 0.6106 (tt0) REVERT: C 507 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6626 (tmm) REVERT: C 658 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.6943 (mmp-170) REVERT: C 737 SER cc_start: 0.8711 (m) cc_final: 0.8509 (p) REVERT: C 1007 PHE cc_start: 0.8787 (t80) cc_final: 0.8547 (t80) REVERT: D 73 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8244 (p) REVERT: D 106 MET cc_start: 0.9132 (mmm) cc_final: 0.8507 (mmm) REVERT: D 155 MET cc_start: 0.8626 (mmm) cc_final: 0.8327 (mmt) REVERT: D 168 TYR cc_start: 0.8807 (m-80) cc_final: 0.8567 (m-80) outliers start: 53 outliers final: 26 residues processed: 261 average time/residue: 0.1623 time to fit residues: 65.5948 Evaluate side-chains 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 259 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 194 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 486 ASN A 904 GLN B 146 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS D 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092586 restraints weight = 33982.022| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.17 r_work: 0.2759 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23160 Z= 0.147 Angle : 0.591 9.487 31336 Z= 0.278 Chirality : 0.044 0.458 3542 Planarity : 0.004 0.042 3806 Dihedral : 13.589 179.875 5308 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.83 % Allowed : 16.49 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2636 helix: 1.74 (0.15), residues: 1196 sheet: -0.11 (0.30), residues: 292 loop : -0.95 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 255 TYR 0.015 0.001 TYR C 488 PHE 0.024 0.002 PHE C 793 TRP 0.028 0.001 TRP A 392 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00351 (23116) covalent geometry : angle 0.56661 (31210) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.69105 ( 12) hydrogen bonds : bond 0.05341 ( 1010) hydrogen bonds : angle 4.09077 ( 2922) link_ALPHA1-3 : bond 0.01071 ( 6) link_ALPHA1-3 : angle 3.79119 ( 18) link_ALPHA1-6 : bond 0.00609 ( 4) link_ALPHA1-6 : angle 1.74862 ( 12) link_BETA1-2 : bond 0.00621 ( 2) link_BETA1-2 : angle 4.36647 ( 6) link_BETA1-4 : bond 0.00745 ( 14) link_BETA1-4 : angle 3.10368 ( 42) link_BETA1-6 : bond 0.00168 ( 4) link_BETA1-6 : angle 1.66651 ( 12) link_NAG-ASN : bond 0.00616 ( 8) link_NAG-ASN : angle 1.37006 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7494 (pt0) REVERT: A 65 ASN cc_start: 0.6511 (m-40) cc_final: 0.6063 (t0) REVERT: A 127 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.5917 (p0) REVERT: A 231 PHE cc_start: 0.7900 (t80) cc_final: 0.7197 (t80) REVERT: A 331 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8639 (m-40) REVERT: A 434 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6620 (mm110) REVERT: A 487 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6980 (mmmt) REVERT: A 534 MET cc_start: 0.7090 (mpp) cc_final: 0.6788 (mpp) REVERT: A 1007 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8426 (t80) REVERT: B 55 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8684 (tp) REVERT: B 180 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8887 (pttm) REVERT: B 243 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8928 (pt0) REVERT: B 286 ASP cc_start: 0.8763 (t0) cc_final: 0.8484 (m-30) REVERT: C 45 LYS cc_start: 0.8369 (mtmm) cc_final: 0.7673 (mttt) REVERT: C 61 ARG cc_start: 0.7931 (tmm160) cc_final: 0.7380 (tmt170) REVERT: C 100 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: C 127 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.5208 (t0) REVERT: C 156 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6569 (mtm180) REVERT: C 158 MET cc_start: 0.8099 (tpp) cc_final: 0.7354 (ttp) REVERT: C 202 ASP cc_start: 0.8000 (m-30) cc_final: 0.7691 (t0) REVERT: C 331 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8576 (m-40) REVERT: C 427 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 487 LYS cc_start: 0.7570 (mmtt) cc_final: 0.7279 (mmmt) REVERT: C 489 GLN cc_start: 0.6601 (tt0) cc_final: 0.6206 (tt0) REVERT: C 578 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: C 589 MET cc_start: 0.8357 (mmm) cc_final: 0.8126 (mtp) REVERT: C 658 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.6993 (mmp-170) REVERT: C 795 ILE cc_start: 0.8748 (mm) cc_final: 0.8429 (mt) REVERT: C 872 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9055 (mt) REVERT: D 13 TRP cc_start: 0.5506 (t60) cc_final: 0.5245 (t-100) REVERT: D 55 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8696 (tp) REVERT: D 106 MET cc_start: 0.9175 (mmm) cc_final: 0.8543 (mmm) outliers start: 64 outliers final: 36 residues processed: 253 average time/residue: 0.1481 time to fit residues: 58.7129 Evaluate side-chains 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 86 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN C 486 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091945 restraints weight = 33993.931| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.19 r_work: 0.2745 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23160 Z= 0.150 Angle : 0.584 9.339 31336 Z= 0.274 Chirality : 0.043 0.426 3542 Planarity : 0.004 0.041 3806 Dihedral : 13.360 179.156 5306 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 16.49 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2636 helix: 1.79 (0.15), residues: 1196 sheet: -0.04 (0.30), residues: 292 loop : -0.87 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.013 0.001 TYR C 869 PHE 0.022 0.002 PHE A 793 TRP 0.019 0.001 TRP A 392 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00359 (23116) covalent geometry : angle 0.56066 (31210) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.50007 ( 12) hydrogen bonds : bond 0.05302 ( 1010) hydrogen bonds : angle 4.06103 ( 2922) link_ALPHA1-3 : bond 0.01125 ( 6) link_ALPHA1-3 : angle 3.69744 ( 18) link_ALPHA1-6 : bond 0.00561 ( 4) link_ALPHA1-6 : angle 1.80871 ( 12) link_BETA1-2 : bond 0.00728 ( 2) link_BETA1-2 : angle 4.25448 ( 6) link_BETA1-4 : bond 0.00773 ( 14) link_BETA1-4 : angle 2.99602 ( 42) link_BETA1-6 : bond 0.00222 ( 4) link_BETA1-6 : angle 1.62808 ( 12) link_NAG-ASN : bond 0.00519 ( 8) link_NAG-ASN : angle 1.31301 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: A 34 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7498 (pt0) REVERT: A 65 ASN cc_start: 0.6558 (m-40) cc_final: 0.5956 (t0) REVERT: A 127 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6032 (p0) REVERT: A 427 LEU cc_start: 0.8916 (mm) cc_final: 0.8695 (mm) REVERT: A 434 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6466 (mm110) REVERT: A 487 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6914 (mmmt) REVERT: A 534 MET cc_start: 0.7286 (mpp) cc_final: 0.6970 (mpp) REVERT: A 558 PHE cc_start: 0.5927 (t80) cc_final: 0.5523 (t80) REVERT: A 1007 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8478 (t80) REVERT: B 21 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: B 55 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8710 (tp) REVERT: B 155 MET cc_start: 0.8734 (mmm) cc_final: 0.8382 (mmt) REVERT: B 180 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8845 (ptpt) REVERT: B 286 ASP cc_start: 0.8768 (t0) cc_final: 0.8504 (m-30) REVERT: C 45 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7702 (mptt) REVERT: C 61 ARG cc_start: 0.7875 (tmm160) cc_final: 0.7347 (tmt170) REVERT: C 100 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: C 127 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.5309 (t0) REVERT: C 156 ARG cc_start: 0.6817 (mtt180) cc_final: 0.6577 (mtm180) REVERT: C 158 MET cc_start: 0.8265 (tpp) cc_final: 0.7559 (ttp) REVERT: C 202 ASP cc_start: 0.7998 (m-30) cc_final: 0.7698 (t0) REVERT: C 331 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8387 (t0) REVERT: C 427 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8786 (mm) REVERT: C 487 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6993 (mmmt) REVERT: C 489 GLN cc_start: 0.6305 (tt0) cc_final: 0.6041 (tt0) REVERT: C 578 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: C 658 ARG cc_start: 0.7465 (mmt-90) cc_final: 0.7100 (mmp-170) REVERT: C 795 ILE cc_start: 0.8745 (mm) cc_final: 0.8454 (mt) REVERT: C 872 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9059 (mt) REVERT: D 13 TRP cc_start: 0.5585 (t60) cc_final: 0.5283 (t-100) REVERT: D 106 MET cc_start: 0.9118 (mmm) cc_final: 0.8825 (mmm) REVERT: D 155 MET cc_start: 0.8804 (mmm) cc_final: 0.8570 (mmm) outliers start: 62 outliers final: 37 residues processed: 254 average time/residue: 0.1632 time to fit residues: 64.6216 Evaluate side-chains 235 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 9 optimal weight: 0.0170 overall best weight: 0.7226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093392 restraints weight = 33682.910| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.12 r_work: 0.2934 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23160 Z= 0.104 Angle : 0.547 9.819 31336 Z= 0.255 Chirality : 0.042 0.439 3542 Planarity : 0.003 0.039 3806 Dihedral : 12.847 179.168 5304 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.99 % Allowed : 17.06 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2636 helix: 1.89 (0.15), residues: 1212 sheet: 0.16 (0.32), residues: 256 loop : -0.78 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.014 0.001 TYR C 488 PHE 0.019 0.001 PHE A 793 TRP 0.020 0.001 TRP A 392 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00228 (23116) covalent geometry : angle 0.52278 (31210) SS BOND : bond 0.00218 ( 6) SS BOND : angle 1.07938 ( 12) hydrogen bonds : bond 0.04402 ( 1010) hydrogen bonds : angle 3.91520 ( 2922) link_ALPHA1-3 : bond 0.01087 ( 6) link_ALPHA1-3 : angle 3.79053 ( 18) link_ALPHA1-6 : bond 0.00632 ( 4) link_ALPHA1-6 : angle 1.80059 ( 12) link_BETA1-2 : bond 0.00730 ( 2) link_BETA1-2 : angle 4.22059 ( 6) link_BETA1-4 : bond 0.00717 ( 14) link_BETA1-4 : angle 2.83253 ( 42) link_BETA1-6 : bond 0.00181 ( 4) link_BETA1-6 : angle 1.46815 ( 12) link_NAG-ASN : bond 0.00680 ( 8) link_NAG-ASN : angle 1.50384 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: A 34 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7545 (pt0) REVERT: A 61 ARG cc_start: 0.7880 (tmm160) cc_final: 0.7254 (ttp-170) REVERT: A 65 ASN cc_start: 0.6539 (m-40) cc_final: 0.5915 (t0) REVERT: A 218 LEU cc_start: 0.9293 (tp) cc_final: 0.9047 (tt) REVERT: A 427 LEU cc_start: 0.8917 (mm) cc_final: 0.8619 (mm) REVERT: A 434 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6481 (mm110) REVERT: A 487 LYS cc_start: 0.7470 (mmtt) cc_final: 0.6902 (mmmt) REVERT: A 534 MET cc_start: 0.7130 (mpp) cc_final: 0.6359 (mpp) REVERT: B 21 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 55 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 155 MET cc_start: 0.8523 (mmm) cc_final: 0.8221 (mmt) REVERT: B 180 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8852 (pttm) REVERT: B 243 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8870 (pt0) REVERT: C 45 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7727 (mptt) REVERT: C 61 ARG cc_start: 0.7716 (tmm160) cc_final: 0.7393 (tmt170) REVERT: C 127 ASN cc_start: 0.6893 (OUTLIER) cc_final: 0.5443 (t0) REVERT: C 158 MET cc_start: 0.8222 (tpp) cc_final: 0.7523 (tpp) REVERT: C 202 ASP cc_start: 0.8001 (m-30) cc_final: 0.7709 (t0) REVERT: C 427 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 487 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7294 (mmmt) REVERT: C 489 GLN cc_start: 0.6604 (tt0) cc_final: 0.6348 (tt0) REVERT: C 578 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.5193 (m-80) REVERT: C 658 ARG cc_start: 0.7367 (mmt-90) cc_final: 0.7011 (mmp-170) REVERT: C 832 MET cc_start: 0.8887 (mmp) cc_final: 0.8650 (mmt) REVERT: C 872 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8994 (mt) REVERT: C 997 ILE cc_start: 0.9057 (tt) cc_final: 0.8826 (pt) REVERT: D 13 TRP cc_start: 0.5582 (t60) cc_final: 0.5311 (t-100) REVERT: D 73 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8269 (p) REVERT: D 106 MET cc_start: 0.9007 (mmm) cc_final: 0.8398 (mmm) REVERT: D 155 MET cc_start: 0.8615 (mmm) cc_final: 0.8405 (mmm) outliers start: 45 outliers final: 27 residues processed: 240 average time/residue: 0.1665 time to fit residues: 61.8679 Evaluate side-chains 221 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 71 optimal weight: 0.0970 chunk 242 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN C 946 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091259 restraints weight = 33982.513| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.11 r_work: 0.2806 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23160 Z= 0.143 Angle : 0.580 9.813 31336 Z= 0.274 Chirality : 0.043 0.420 3542 Planarity : 0.004 0.041 3806 Dihedral : 12.769 177.001 5299 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 17.42 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2636 helix: 1.84 (0.15), residues: 1208 sheet: 0.10 (0.31), residues: 262 loop : -0.72 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.017 0.001 TYR A 684 PHE 0.023 0.002 PHE C 793 TRP 0.018 0.001 TRP A 392 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00342 (23116) covalent geometry : angle 0.55688 (31210) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.55344 ( 12) hydrogen bonds : bond 0.05182 ( 1010) hydrogen bonds : angle 3.98926 ( 2922) link_ALPHA1-3 : bond 0.00929 ( 6) link_ALPHA1-3 : angle 3.75834 ( 18) link_ALPHA1-6 : bond 0.00564 ( 4) link_ALPHA1-6 : angle 1.82205 ( 12) link_BETA1-2 : bond 0.00777 ( 2) link_BETA1-2 : angle 4.17183 ( 6) link_BETA1-4 : bond 0.00753 ( 14) link_BETA1-4 : angle 2.88452 ( 42) link_BETA1-6 : bond 0.00169 ( 4) link_BETA1-6 : angle 1.64023 ( 12) link_NAG-ASN : bond 0.00769 ( 8) link_NAG-ASN : angle 1.65246 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: A 34 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7535 (pt0) REVERT: A 61 ARG cc_start: 0.7893 (tmm160) cc_final: 0.7256 (ttp-170) REVERT: A 65 ASN cc_start: 0.6546 (m-40) cc_final: 0.5906 (t0) REVERT: A 427 LEU cc_start: 0.8905 (mm) cc_final: 0.8599 (mm) REVERT: A 487 LYS cc_start: 0.7464 (mmtt) cc_final: 0.7160 (mmmt) REVERT: A 534 MET cc_start: 0.6744 (mpp) cc_final: 0.6369 (mpp) REVERT: B 26 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8893 (mt) REVERT: B 55 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8705 (tp) REVERT: B 155 MET cc_start: 0.8577 (mmm) cc_final: 0.8217 (mmt) REVERT: B 180 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8919 (pttm) REVERT: B 243 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: C 45 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7716 (mptt) REVERT: C 61 ARG cc_start: 0.7701 (tmm160) cc_final: 0.7233 (ttp80) REVERT: C 158 MET cc_start: 0.8259 (tpp) cc_final: 0.7707 (ttp) REVERT: C 202 ASP cc_start: 0.8013 (m-30) cc_final: 0.7693 (t0) REVERT: C 427 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 487 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7320 (mmmt) REVERT: C 489 GLN cc_start: 0.6665 (tt0) cc_final: 0.6333 (tt0) REVERT: C 578 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.4894 (m-80) REVERT: C 872 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9048 (mt) REVERT: C 997 ILE cc_start: 0.9127 (tt) cc_final: 0.8866 (pt) outliers start: 41 outliers final: 27 residues processed: 225 average time/residue: 0.1621 time to fit residues: 56.8428 Evaluate side-chains 220 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 230 optimal weight: 0.0970 chunk 252 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094825 restraints weight = 33917.835| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.23 r_work: 0.2929 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23160 Z= 0.102 Angle : 0.547 10.829 31336 Z= 0.254 Chirality : 0.042 0.430 3542 Planarity : 0.003 0.038 3806 Dihedral : 12.250 178.634 5297 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.19 % Allowed : 18.30 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2636 helix: 2.02 (0.15), residues: 1214 sheet: 0.19 (0.32), residues: 262 loop : -0.69 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 67 TYR 0.013 0.001 TYR C 869 PHE 0.020 0.001 PHE A 558 TRP 0.018 0.001 TRP A 392 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00224 (23116) covalent geometry : angle 0.52244 (31210) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.43435 ( 12) hydrogen bonds : bond 0.04113 ( 1010) hydrogen bonds : angle 3.87075 ( 2922) link_ALPHA1-3 : bond 0.01005 ( 6) link_ALPHA1-3 : angle 3.87719 ( 18) link_ALPHA1-6 : bond 0.00634 ( 4) link_ALPHA1-6 : angle 1.83214 ( 12) link_BETA1-2 : bond 0.00768 ( 2) link_BETA1-2 : angle 4.12133 ( 6) link_BETA1-4 : bond 0.00698 ( 14) link_BETA1-4 : angle 2.72033 ( 42) link_BETA1-6 : bond 0.00174 ( 4) link_BETA1-6 : angle 1.47639 ( 12) link_NAG-ASN : bond 0.00741 ( 8) link_NAG-ASN : angle 1.66093 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7404 (pt0) REVERT: A 61 ARG cc_start: 0.7900 (tmm160) cc_final: 0.7300 (ttp80) REVERT: A 65 ASN cc_start: 0.6582 (m-40) cc_final: 0.5923 (t0) REVERT: A 170 LEU cc_start: 0.8397 (mt) cc_final: 0.8182 (mm) REVERT: A 427 LEU cc_start: 0.8886 (mm) cc_final: 0.8602 (mm) REVERT: A 487 LYS cc_start: 0.7475 (mmtt) cc_final: 0.6918 (mmmt) REVERT: A 534 MET cc_start: 0.6811 (mpp) cc_final: 0.6511 (mpp) REVERT: A 615 MET cc_start: 0.8809 (ttt) cc_final: 0.8555 (ttt) REVERT: B 26 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8857 (mt) REVERT: B 155 MET cc_start: 0.8570 (mmm) cc_final: 0.8285 (mmt) REVERT: B 180 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8828 (pttm) REVERT: C 45 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7710 (mptt) REVERT: C 61 ARG cc_start: 0.7638 (tmm160) cc_final: 0.7079 (ttp80) REVERT: C 158 MET cc_start: 0.8214 (tpp) cc_final: 0.7498 (tpp) REVERT: C 202 ASP cc_start: 0.7960 (m-30) cc_final: 0.7642 (t0) REVERT: C 427 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 489 GLN cc_start: 0.6747 (tt0) cc_final: 0.6367 (tt0) REVERT: C 578 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: C 615 MET cc_start: 0.8816 (ttt) cc_final: 0.8548 (ttt) REVERT: C 872 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8972 (mt) REVERT: C 997 ILE cc_start: 0.9082 (tt) cc_final: 0.8876 (pt) REVERT: C 1007 PHE cc_start: 0.8743 (t80) cc_final: 0.8491 (t80) REVERT: D 106 MET cc_start: 0.9032 (mmm) cc_final: 0.8483 (mmm) REVERT: D 155 MET cc_start: 0.8696 (mmm) cc_final: 0.8407 (mmt) outliers start: 27 outliers final: 20 residues processed: 218 average time/residue: 0.1653 time to fit residues: 55.6604 Evaluate side-chains 211 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1011 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 203 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS A 904 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092918 restraints weight = 34010.652| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.16 r_work: 0.2826 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23160 Z= 0.118 Angle : 0.560 11.746 31336 Z= 0.261 Chirality : 0.042 0.425 3542 Planarity : 0.004 0.040 3806 Dihedral : 12.106 177.289 5290 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.06 % Allowed : 18.66 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2636 helix: 1.99 (0.15), residues: 1212 sheet: 0.24 (0.31), residues: 270 loop : -0.65 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 67 TYR 0.013 0.001 TYR C 869 PHE 0.021 0.001 PHE A 793 TRP 0.019 0.001 TRP A 392 HIS 0.004 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00275 (23116) covalent geometry : angle 0.53692 (31210) SS BOND : bond 0.00192 ( 6) SS BOND : angle 1.33127 ( 12) hydrogen bonds : bond 0.04528 ( 1010) hydrogen bonds : angle 3.89740 ( 2922) link_ALPHA1-3 : bond 0.00937 ( 6) link_ALPHA1-3 : angle 3.85899 ( 18) link_ALPHA1-6 : bond 0.00593 ( 4) link_ALPHA1-6 : angle 1.84426 ( 12) link_BETA1-2 : bond 0.00808 ( 2) link_BETA1-2 : angle 4.10252 ( 6) link_BETA1-4 : bond 0.00719 ( 14) link_BETA1-4 : angle 2.70768 ( 42) link_BETA1-6 : bond 0.00182 ( 4) link_BETA1-6 : angle 1.54170 ( 12) link_NAG-ASN : bond 0.00688 ( 8) link_NAG-ASN : angle 1.66837 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5954.62 seconds wall clock time: 102 minutes 23.83 seconds (6143.83 seconds total)