Starting phenix.real_space_refine on Thu Mar 5 15:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyv_32895/03_2026/7wyv_32895.map" } resolution = 3.7 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= 0.004 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 32 5.49 5 Mg 4 5.21 5 S 118 5.16 5 Na 2 4.78 5 C 14652 2.51 5 N 3524 2.21 5 O 4336 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: 22668 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 2, ' NA': 1, 'ATP': 1, 'CLR': 3, 'PCW': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: C, D, E, K, L, M, N Time building chain proxies: 9.94, per 1000 atoms: 0.44 Number of scatterers: 22668 At special positions: 0 Unit cell: (216.276, 179.692, 103.296, 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 32 15.00 Mg 4 11.99 Na 2 11.00 O 4336 8.00 N 3524 7.00 C 14652 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: 2.19 Conformation dependent library (CDL) restraints added in 864.3 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: 110 helices and 20 sheets defined 49.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 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 89 through 97 removed outlier: 3.769A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (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 removed outlier: 3.853A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.663A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.615A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 4.000A 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: 3.652A 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 removed outlier: 3.502A pdb=" N LEU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.801A 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: 3.696A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.133A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) 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 756 through 782 removed outlier: 3.756A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 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: 3.653A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.646A 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: 4.227A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 4.041A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.347A 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: 3.553A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.789A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.534A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.796A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.548A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.909A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.363A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.755A 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: 4.203A 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 89 through 97 removed outlier: 3.768A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (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 removed outlier: 3.854A pdb=" N ILE C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.663A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.615A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 4.000A 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: 3.651A 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 removed outlier: 3.502A pdb=" N LEU C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.802A 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: 3.696A 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: 3.654A 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 756 through 782 removed outlier: 3.756A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 797 Proline residue: C 789 - end of helix Processing helix chain 'C' and resid 803 through 812 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: 3.653A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.647A 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: 4.227A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 4.040A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.347A 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: 3.553A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.789A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.534A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.796A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.548A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.909A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.363A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.756A 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: 4.203A 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: 11.769A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.731A 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: 4.174A 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: 6.651A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.241A 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: 6.483A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.245A 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: 3.889A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 448 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.562A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.119A 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: 11.769A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.911A 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: 6.730A 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: 4.174A 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: 6.652A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.245A 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: 3.889A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 448 " --> pdb=" O VAL C 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.563A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.119A 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 125 998 hydrogen bonds defined for protein. 2892 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: 3.91 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6867 1.35 - 1.47: 5220 1.47 - 1.59: 10763 1.59 - 1.71: 68 1.71 - 1.83: 172 Bond restraints: 23090 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" C39 PCW A1114 " pdb=" C40 PCW A1114 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW C1114 " pdb=" C40 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C19 PCW A1110 " pdb=" C20 PCW A1110 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 29091 2.33 - 4.67: 1634 4.67 - 7.00: 289 7.00 - 9.34: 102 9.34 - 11.67: 46 Bond angle restraints: 31162 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 106.65 6.47 1.25e+00 6.40e-01 2.68e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 106.71 6.41 1.25e+00 6.40e-01 2.63e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.46e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C SER D 122 " pdb=" N PRO D 123 " pdb=" CA PRO D 123 " ideal model delta sigma weight residual 127.00 115.44 11.56 2.40e+00 1.74e-01 2.32e+01 ... (remaining 31157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14080 35.94 - 71.89: 796 71.89 - 107.83: 86 107.83 - 143.78: 40 143.78 - 179.72: 2 Dihedral angle restraints: 15004 sinusoidal: 7348 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.55 -179.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.52 -179.69 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual -168.17 -29.69 -138.48 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2920 0.074 - 0.148: 497 0.148 - 0.222: 59 0.222 - 0.296: 24 0.296 - 0.370: 20 Chirality restraints: 3520 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 -2.25 -0.15 2.00e-02 2.50e+03 5.91e+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 -2.25 -0.15 2.00e-02 2.50e+03 5.69e+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 -2.33 -0.07 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3517 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO C 283 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO A 283 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 594 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO A 595 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " -0.046 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 144 2.54 - 3.13: 17053 3.13 - 3.72: 31849 3.72 - 4.31: 46883 4.31 - 4.90: 76918 Nonbonded interactions: 172847 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.954 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.954 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1202 " model vdw 1.994 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 2.003 2.170 nonbonded pdb=" O THR C 378 " pdb="MG MG C1101 " model vdw 2.020 2.170 ... (remaining 172842 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 group one per residue 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 0.308 23134 Z= 0.540 Angle : 1.322 17.282 31288 Z= 0.620 Chirality : 0.063 0.370 3520 Planarity : 0.008 0.105 3806 Dihedral : 20.330 179.724 10074 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 10.52 % Allowed : 8.36 % Favored : 81.12 % 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: -3.15 (0.14), residues: 2636 helix: -1.48 (0.13), residues: 1192 sheet: -2.36 (0.28), residues: 266 loop : -2.61 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.035 0.002 TYR D 40 PHE 0.023 0.002 PHE D 297 TRP 0.027 0.002 TRP C 894 HIS 0.009 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.01072 (23090) covalent geometry : angle 1.29743 (31162) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.89163 ( 12) hydrogen bonds : bond 0.15774 ( 998) hydrogen bonds : angle 7.01497 ( 2892) link_ALPHA1-3 : bond 0.00760 ( 6) link_ALPHA1-3 : angle 3.08011 ( 18) link_ALPHA1-6 : bond 0.00655 ( 4) link_ALPHA1-6 : angle 1.31781 ( 12) link_BETA1-2 : bond 0.00763 ( 2) link_BETA1-2 : angle 5.45504 ( 6) link_BETA1-4 : bond 0.00837 ( 14) link_BETA1-4 : angle 5.94233 ( 42) link_BETA1-6 : bond 0.00216 ( 4) link_BETA1-6 : angle 1.02265 ( 12) link_NAG-ASN : bond 0.01367 ( 8) link_NAG-ASN : angle 3.42088 ( 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 717 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 479 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4443 (tp) REVERT: A 64 THR cc_start: 0.4284 (OUTLIER) cc_final: 0.3832 (p) REVERT: A 127 ASN cc_start: 0.3716 (OUTLIER) cc_final: 0.3473 (t0) REVERT: A 180 ILE cc_start: 0.6921 (pt) cc_final: 0.6662 (tp) REVERT: A 240 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7798 (mtt180) REVERT: A 241 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7800 (p0) REVERT: A 260 TYR cc_start: 0.7321 (m-80) cc_final: 0.6735 (m-80) REVERT: A 493 HIS cc_start: 0.4723 (OUTLIER) cc_final: 0.3415 (m-70) REVERT: A 515 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7261 (pp) REVERT: A 524 ASN cc_start: 0.8008 (t0) cc_final: 0.7593 (t0) REVERT: A 753 ASP cc_start: 0.7235 (m-30) cc_final: 0.6954 (m-30) REVERT: A 837 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7024 (ptt-90) REVERT: A 923 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 32 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7158 (t) REVERT: B 73 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7463 (p) REVERT: B 94 SER cc_start: 0.6957 (OUTLIER) cc_final: 0.6540 (p) REVERT: B 284 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7448 (p0) REVERT: C 63 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4688 (tp) REVERT: C 174 ASP cc_start: 0.7076 (t0) cc_final: 0.6305 (m-30) REVERT: C 180 ILE cc_start: 0.7228 (pt) cc_final: 0.6783 (tp) REVERT: C 240 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: C 272 THR cc_start: 0.7851 (m) cc_final: 0.7619 (p) REVERT: C 381 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 489 GLN cc_start: 0.7815 (tt0) cc_final: 0.7029 (tt0) REVERT: C 493 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.2973 (m-70) REVERT: C 515 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7262 (pp) REVERT: C 524 ASN cc_start: 0.7894 (t0) cc_final: 0.7438 (p0) REVERT: C 692 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6253 (tpt170) REVERT: C 837 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7248 (ptt-90) REVERT: C 923 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (t80) REVERT: D 32 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (t) REVERT: D 73 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7434 (p) REVERT: D 94 SER cc_start: 0.7062 (OUTLIER) cc_final: 0.6663 (p) REVERT: D 284 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7409 (p0) outliers start: 238 outliers final: 28 residues processed: 654 average time/residue: 0.1798 time to fit residues: 173.0694 Evaluate side-chains 272 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 37 PHE 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 284 ASN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 484 SER 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 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 788 THR 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 923 PHE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 434 GLN A 656 ASN A 683 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN A 904 GLN A1019 GLN B 56 GLN B 70 GLN B 258 GLN C 225 GLN C 406 GLN C 434 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 GLN C 683 HIS C 754 ASN C 826 GLN C 904 GLN C1019 GLN D 56 GLN D 70 GLN D 258 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.118889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091099 restraints weight = 51891.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091141 restraints weight = 32076.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092060 restraints weight = 24750.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092572 restraints weight = 23336.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092578 restraints weight = 20191.532| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23134 Z= 0.176 Angle : 0.738 10.741 31288 Z= 0.356 Chirality : 0.048 0.425 3520 Planarity : 0.006 0.069 3806 Dihedral : 17.125 172.679 5216 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.76 % Allowed : 14.15 % Favored : 82.10 % 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: -1.30 (0.15), residues: 2636 helix: 0.30 (0.15), residues: 1206 sheet: -1.99 (0.29), residues: 228 loop : -1.85 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 889 TYR 0.019 0.002 TYR D 40 PHE 0.026 0.002 PHE C 571 TRP 0.020 0.002 TRP A 392 HIS 0.005 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00397 (23090) covalent geometry : angle 0.71216 (31162) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.09143 ( 12) hydrogen bonds : bond 0.05761 ( 998) hydrogen bonds : angle 5.05262 ( 2892) link_ALPHA1-3 : bond 0.01106 ( 6) link_ALPHA1-3 : angle 3.90499 ( 18) link_ALPHA1-6 : bond 0.00821 ( 4) link_ALPHA1-6 : angle 2.17685 ( 12) link_BETA1-2 : bond 0.00547 ( 2) link_BETA1-2 : angle 4.62242 ( 6) link_BETA1-4 : bond 0.00913 ( 14) link_BETA1-4 : angle 3.75814 ( 42) link_BETA1-6 : bond 0.00631 ( 4) link_BETA1-6 : angle 1.61846 ( 12) link_NAG-ASN : bond 0.00778 ( 8) link_NAG-ASN : angle 2.34669 ( 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 305 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 220 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6353 (ppp) cc_final: 0.5597 (ppp) REVERT: A 64 THR cc_start: 0.4292 (OUTLIER) cc_final: 0.3458 (p) REVERT: A 260 TYR cc_start: 0.7405 (m-80) cc_final: 0.7172 (m-80) REVERT: A 493 HIS cc_start: 0.4586 (OUTLIER) cc_final: 0.3574 (m-70) REVERT: A 494 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5966 (pm20) REVERT: A 524 ASN cc_start: 0.8055 (t0) cc_final: 0.7544 (p0) REVERT: A 837 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7586 (ptt-90) REVERT: B 73 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.7709 (p) REVERT: B 94 SER cc_start: 0.7345 (OUTLIER) cc_final: 0.6867 (p) REVERT: B 284 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7219 (p0) REVERT: G 15 ASP cc_start: 0.7504 (t0) cc_final: 0.7267 (t70) REVERT: C 64 THR cc_start: 0.3901 (OUTLIER) cc_final: 0.3678 (t) REVERT: C 230 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: C 272 THR cc_start: 0.8169 (m) cc_final: 0.7711 (p) REVERT: C 483 ASN cc_start: 0.5635 (t0) cc_final: 0.5389 (t0) REVERT: C 493 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.3303 (m-70) REVERT: C 524 ASN cc_start: 0.7829 (t0) cc_final: 0.7326 (p0) REVERT: C 530 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5934 (tt) REVERT: C 534 MET cc_start: 0.6219 (mmp) cc_final: 0.5683 (mpp) REVERT: C 837 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7739 (ptt-90) REVERT: D 73 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 94 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6627 (p) REVERT: D 284 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7219 (p0) outliers start: 85 outliers final: 37 residues processed: 297 average time/residue: 0.1580 time to fit residues: 73.2057 Evaluate side-chains 218 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU 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 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 383 GLN A 754 ASN C 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088002 restraints weight = 51185.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087892 restraints weight = 33531.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088842 restraints weight = 25925.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.089157 restraints weight = 23474.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.089177 restraints weight = 22312.263| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23134 Z= 0.162 Angle : 0.644 9.631 31288 Z= 0.310 Chirality : 0.045 0.419 3520 Planarity : 0.005 0.055 3806 Dihedral : 15.799 156.115 5162 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.58 % Allowed : 15.30 % Favored : 81.12 % 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: -0.46 (0.16), residues: 2636 helix: 0.90 (0.15), residues: 1224 sheet: -1.29 (0.32), residues: 228 loop : -1.39 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.022 0.001 TYR A 488 PHE 0.016 0.002 PHE C 184 TRP 0.023 0.002 TRP A 418 HIS 0.006 0.001 HIS C 620 Details of bonding type rmsd covalent geometry : bond 0.00376 (23090) covalent geometry : angle 0.61891 (31162) SS BOND : bond 0.00363 ( 6) SS BOND : angle 1.63626 ( 12) hydrogen bonds : bond 0.05404 ( 998) hydrogen bonds : angle 4.55616 ( 2892) link_ALPHA1-3 : bond 0.01124 ( 6) link_ALPHA1-3 : angle 3.38276 ( 18) link_ALPHA1-6 : bond 0.00827 ( 4) link_ALPHA1-6 : angle 1.64265 ( 12) link_BETA1-2 : bond 0.00468 ( 2) link_BETA1-2 : angle 4.36179 ( 6) link_BETA1-4 : bond 0.01111 ( 14) link_BETA1-4 : angle 3.35572 ( 42) link_BETA1-6 : bond 0.00363 ( 4) link_BETA1-6 : angle 1.56111 ( 12) link_NAG-ASN : bond 0.00613 ( 8) link_NAG-ASN : angle 2.38804 ( 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 258 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 177 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6398 (ppp) cc_final: 0.5964 (ppp) REVERT: A 260 TYR cc_start: 0.7392 (m-80) cc_final: 0.7117 (m-10) REVERT: A 418 TRP cc_start: 0.6881 (t-100) cc_final: 0.6635 (t-100) REVERT: A 493 HIS cc_start: 0.4352 (OUTLIER) cc_final: 0.3224 (m-70) REVERT: A 524 ASN cc_start: 0.8114 (t0) cc_final: 0.7573 (t0) REVERT: A 605 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7626 (mtpt) REVERT: B 73 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.7747 (p) REVERT: C 230 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: C 272 THR cc_start: 0.8227 (m) cc_final: 0.7856 (p) REVERT: C 476 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7532 (tttp) REVERT: C 483 ASN cc_start: 0.5326 (t0) cc_final: 0.5110 (t0) REVERT: C 493 HIS cc_start: 0.4357 (OUTLIER) cc_final: 0.3164 (m-70) REVERT: C 524 ASN cc_start: 0.7943 (t0) cc_final: 0.7400 (p0) REVERT: C 692 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7360 (tpm170) REVERT: D 73 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.7674 (p) outliers start: 81 outliers final: 42 residues processed: 249 average time/residue: 0.1578 time to fit residues: 61.9797 Evaluate side-chains 197 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 258 optimal weight: 0.4980 chunk 214 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 384 ASN A 406 GLN B 264 GLN G 8 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN E 8 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088774 restraints weight = 50732.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088697 restraints weight = 33006.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089338 restraints weight = 25593.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089870 restraints weight = 24723.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089934 restraints weight = 21990.795| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23134 Z= 0.117 Angle : 0.583 9.445 31288 Z= 0.275 Chirality : 0.044 0.447 3520 Planarity : 0.004 0.050 3806 Dihedral : 14.580 126.978 5144 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.79 % Allowed : 16.09 % Favored : 81.12 % 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: 0.03 (0.16), residues: 2636 helix: 1.35 (0.15), residues: 1224 sheet: -0.90 (0.33), residues: 226 loop : -1.22 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.010 0.001 TYR C 869 PHE 0.020 0.001 PHE A 231 TRP 0.022 0.001 TRP C 418 HIS 0.005 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00258 (23090) covalent geometry : angle 0.55710 (31162) SS BOND : bond 0.00054 ( 6) SS BOND : angle 1.02823 ( 12) hydrogen bonds : bond 0.04509 ( 998) hydrogen bonds : angle 4.24377 ( 2892) link_ALPHA1-3 : bond 0.01116 ( 6) link_ALPHA1-3 : angle 3.68202 ( 18) link_ALPHA1-6 : bond 0.00851 ( 4) link_ALPHA1-6 : angle 1.69777 ( 12) link_BETA1-2 : bond 0.00381 ( 2) link_BETA1-2 : angle 4.45545 ( 6) link_BETA1-4 : bond 0.00643 ( 14) link_BETA1-4 : angle 3.20211 ( 42) link_BETA1-6 : bond 0.00223 ( 4) link_BETA1-6 : angle 1.50788 ( 12) link_NAG-ASN : bond 0.00538 ( 8) link_NAG-ASN : angle 2.02278 ( 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 236 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6365 (ppp) cc_final: 0.6049 (ppp) REVERT: A 63 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4403 (mp) REVERT: A 173 ARG cc_start: 0.4959 (OUTLIER) cc_final: 0.4651 (ptp90) REVERT: A 331 ASN cc_start: 0.8406 (t0) cc_final: 0.8112 (t0) REVERT: A 418 TRP cc_start: 0.6963 (t-100) cc_final: 0.6640 (t-100) REVERT: A 493 HIS cc_start: 0.4379 (OUTLIER) cc_final: 0.3626 (m-70) REVERT: A 524 ASN cc_start: 0.8074 (t0) cc_final: 0.7439 (t0) REVERT: A 530 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6221 (tt) REVERT: A 605 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7607 (mtmt) REVERT: A 659 ASP cc_start: 0.7243 (m-30) cc_final: 0.6754 (p0) REVERT: A 852 MET cc_start: 0.8348 (mmm) cc_final: 0.7988 (mmp) REVERT: C 230 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: C 476 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7581 (ttmm) REVERT: C 483 ASN cc_start: 0.5463 (t0) cc_final: 0.5191 (t0) REVERT: C 493 HIS cc_start: 0.4282 (OUTLIER) cc_final: 0.3051 (m-70) REVERT: C 524 ASN cc_start: 0.8034 (t0) cc_final: 0.7432 (p0) REVERT: C 534 MET cc_start: 0.6202 (mmt) cc_final: 0.5835 (mpp) REVERT: C 605 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7437 (mtmt) REVERT: C 692 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7206 (tpm170) outliers start: 63 outliers final: 39 residues processed: 226 average time/residue: 0.1620 time to fit residues: 57.1295 Evaluate side-chains 203 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 518 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL 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 144 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 207 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.1604 ------------------------------------------------------------------------------- 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 406 GLN A 474 ASN C 52 HIS C 384 ASN E 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089066 restraints weight = 50606.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088126 restraints weight = 32441.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088950 restraints weight = 25528.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.089438 restraints weight = 24755.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089534 restraints weight = 22584.453| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23134 Z= 0.107 Angle : 0.561 8.819 31288 Z= 0.263 Chirality : 0.043 0.469 3520 Planarity : 0.004 0.051 3806 Dihedral : 13.941 110.468 5134 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.39 % Allowed : 16.53 % Favored : 81.08 % 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: 1.53 (0.15), residues: 1224 sheet: -0.60 (0.32), residues: 246 loop : -1.09 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 517 TYR 0.011 0.001 TYR C 869 PHE 0.017 0.001 PHE C 184 TRP 0.017 0.001 TRP C 418 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00234 (23090) covalent geometry : angle 0.53527 (31162) SS BOND : bond 0.00039 ( 6) SS BOND : angle 0.79920 ( 12) hydrogen bonds : bond 0.04274 ( 998) hydrogen bonds : angle 4.11478 ( 2892) link_ALPHA1-3 : bond 0.01077 ( 6) link_ALPHA1-3 : angle 3.69326 ( 18) link_ALPHA1-6 : bond 0.00816 ( 4) link_ALPHA1-6 : angle 1.61638 ( 12) link_BETA1-2 : bond 0.00423 ( 2) link_BETA1-2 : angle 4.41569 ( 6) link_BETA1-4 : bond 0.00591 ( 14) link_BETA1-4 : angle 3.05140 ( 42) link_BETA1-6 : bond 0.00205 ( 4) link_BETA1-6 : angle 1.50411 ( 12) link_NAG-ASN : bond 0.00487 ( 8) link_NAG-ASN : angle 1.95733 ( 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 218 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6259 (ppp) cc_final: 0.5914 (ppp) REVERT: A 173 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5189 (ptp90) REVERT: A 493 HIS cc_start: 0.4486 (OUTLIER) cc_final: 0.3598 (m-70) REVERT: A 524 ASN cc_start: 0.8183 (t0) cc_final: 0.7534 (t0) REVERT: A 605 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7599 (mtmt) REVERT: A 659 ASP cc_start: 0.7270 (m-30) cc_final: 0.6789 (p0) REVERT: A 852 MET cc_start: 0.8258 (mmm) cc_final: 0.8017 (mmp) REVERT: C 38 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7572 (mt-10) REVERT: C 230 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: C 476 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7683 (ttmm) REVERT: C 483 ASN cc_start: 0.5846 (t0) cc_final: 0.5560 (t0) REVERT: C 493 HIS cc_start: 0.4169 (OUTLIER) cc_final: 0.3089 (m-70) REVERT: C 524 ASN cc_start: 0.8138 (t0) cc_final: 0.7471 (t0) REVERT: C 530 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6453 (tt) REVERT: C 534 MET cc_start: 0.6251 (mmt) cc_final: 0.5878 (mpp) REVERT: C 605 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7502 (mtmt) REVERT: C 692 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7189 (tpm170) outliers start: 54 outliers final: 35 residues processed: 209 average time/residue: 0.1675 time to fit residues: 54.4088 Evaluate side-chains 190 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 518 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 406 GLN B 70 GLN B 146 GLN B 264 GLN D 70 GLN D 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.109646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081683 restraints weight = 51682.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080785 restraints weight = 45025.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081980 restraints weight = 34662.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082409 restraints weight = 27212.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082612 restraints weight = 24807.657| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 23134 Z= 0.287 Angle : 0.784 9.257 31288 Z= 0.379 Chirality : 0.050 0.535 3520 Planarity : 0.005 0.049 3806 Dihedral : 14.541 127.568 5132 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.23 % Allowed : 16.84 % Favored : 79.93 % 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: -0.22 (0.16), residues: 2636 helix: 0.94 (0.15), residues: 1210 sheet: -0.96 (0.31), residues: 266 loop : -1.07 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 911 TYR 0.020 0.002 TYR D 248 PHE 0.029 0.003 PHE A 291 TRP 0.020 0.002 TRP C 418 HIS 0.064 0.003 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00691 (23090) covalent geometry : angle 0.76371 (31162) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.13024 ( 12) hydrogen bonds : bond 0.06884 ( 998) hydrogen bonds : angle 4.74133 ( 2892) link_ALPHA1-3 : bond 0.00933 ( 6) link_ALPHA1-3 : angle 3.90605 ( 18) link_ALPHA1-6 : bond 0.00956 ( 4) link_ALPHA1-6 : angle 1.66010 ( 12) link_BETA1-2 : bond 0.00316 ( 2) link_BETA1-2 : angle 4.20820 ( 6) link_BETA1-4 : bond 0.00581 ( 14) link_BETA1-4 : angle 3.00046 ( 42) link_BETA1-6 : bond 0.00344 ( 4) link_BETA1-6 : angle 1.94405 ( 12) link_NAG-ASN : bond 0.00251 ( 8) link_NAG-ASN : angle 2.93152 ( 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 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 158 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6268 (ppp) cc_final: 0.6038 (ppp) REVERT: A 173 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.4573 (ptp90) REVERT: A 493 HIS cc_start: 0.4706 (OUTLIER) cc_final: 0.3737 (m-70) REVERT: A 524 ASN cc_start: 0.8128 (t0) cc_final: 0.7466 (t0) REVERT: B 47 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7788 (mp) REVERT: B 146 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7545 (mm-40) REVERT: B 156 TRP cc_start: 0.7940 (m-90) cc_final: 0.7608 (m-90) REVERT: C 38 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7834 (mt-10) REVERT: C 173 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.4531 (ptp90) REVERT: C 230 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: C 483 ASN cc_start: 0.5339 (t0) cc_final: 0.5003 (t0) REVERT: C 524 ASN cc_start: 0.8036 (t0) cc_final: 0.7278 (t0) REVERT: C 534 MET cc_start: 0.5985 (mmt) cc_final: 0.5747 (mpp) REVERT: C 605 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7928 (mtmt) REVERT: D 47 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 156 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (m-90) outliers start: 73 outliers final: 44 residues processed: 222 average time/residue: 0.1695 time to fit residues: 58.0882 Evaluate side-chains 194 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 132 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN C 52 HIS D 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084111 restraints weight = 51468.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083487 restraints weight = 36983.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084453 restraints weight = 30488.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084682 restraints weight = 25586.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084854 restraints weight = 23978.279| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23134 Z= 0.136 Angle : 0.604 10.113 31288 Z= 0.287 Chirality : 0.045 0.503 3520 Planarity : 0.004 0.045 3806 Dihedral : 13.864 119.031 5130 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.39 % Allowed : 18.61 % Favored : 79.00 % 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: 0.18 (0.16), residues: 2636 helix: 1.37 (0.15), residues: 1212 sheet: -0.73 (0.32), residues: 266 loop : -1.00 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 517 TYR 0.012 0.001 TYR C 569 PHE 0.031 0.001 PHE C 184 TRP 0.032 0.001 TRP C 418 HIS 0.021 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00312 (23090) covalent geometry : angle 0.58162 (31162) SS BOND : bond 0.00078 ( 6) SS BOND : angle 0.82719 ( 12) hydrogen bonds : bond 0.05214 ( 998) hydrogen bonds : angle 4.28907 ( 2892) link_ALPHA1-3 : bond 0.00951 ( 6) link_ALPHA1-3 : angle 3.79592 ( 18) link_ALPHA1-6 : bond 0.00780 ( 4) link_ALPHA1-6 : angle 1.63162 ( 12) link_BETA1-2 : bond 0.00363 ( 2) link_BETA1-2 : angle 4.37129 ( 6) link_BETA1-4 : bond 0.00520 ( 14) link_BETA1-4 : angle 2.71245 ( 42) link_BETA1-6 : bond 0.00204 ( 4) link_BETA1-6 : angle 1.67336 ( 12) link_NAG-ASN : bond 0.00353 ( 8) link_NAG-ASN : angle 2.32781 ( 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 210 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7772 (mt-10) REVERT: A 173 ARG cc_start: 0.5075 (OUTLIER) cc_final: 0.4685 (ptp90) REVERT: A 260 TYR cc_start: 0.7302 (m-10) cc_final: 0.7049 (m-10) REVERT: A 524 ASN cc_start: 0.8268 (t0) cc_final: 0.7616 (t0) REVERT: B 156 TRP cc_start: 0.7872 (m-90) cc_final: 0.7571 (m-90) REVERT: C 38 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7819 (mt-10) REVERT: C 172 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5448 (tp) REVERT: C 230 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: C 483 ASN cc_start: 0.5543 (t0) cc_final: 0.5231 (t0) REVERT: C 524 ASN cc_start: 0.8118 (t0) cc_final: 0.7378 (t0) REVERT: D 156 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7659 (m-90) outliers start: 54 outliers final: 42 residues processed: 198 average time/residue: 0.1632 time to fit residues: 49.9733 Evaluate side-chains 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 203 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.0020 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 406 GLN B 146 GLN C 52 HIS D 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.111499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083653 restraints weight = 49722.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083448 restraints weight = 31947.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083735 restraints weight = 23629.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084120 restraints weight = 22296.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084425 restraints weight = 21428.101| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23134 Z= 0.190 Angle : 0.638 10.572 31288 Z= 0.304 Chirality : 0.046 0.520 3520 Planarity : 0.004 0.047 3806 Dihedral : 13.730 121.876 5126 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.96 % Allowed : 18.13 % Favored : 78.91 % 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: 0.14 (0.16), residues: 2636 helix: 1.32 (0.15), residues: 1212 sheet: -0.73 (0.31), residues: 266 loop : -1.02 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 517 TYR 0.015 0.002 TYR A 869 PHE 0.027 0.002 PHE C 184 TRP 0.040 0.002 TRP C 418 HIS 0.030 0.002 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00458 (23090) covalent geometry : angle 0.61690 (31162) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.85758 ( 12) hydrogen bonds : bond 0.05426 ( 998) hydrogen bonds : angle 4.39743 ( 2892) link_ALPHA1-3 : bond 0.00834 ( 6) link_ALPHA1-3 : angle 3.83544 ( 18) link_ALPHA1-6 : bond 0.00769 ( 4) link_ALPHA1-6 : angle 1.69378 ( 12) link_BETA1-2 : bond 0.00335 ( 2) link_BETA1-2 : angle 4.26292 ( 6) link_BETA1-4 : bond 0.00549 ( 14) link_BETA1-4 : angle 2.68848 ( 42) link_BETA1-6 : bond 0.00167 ( 4) link_BETA1-6 : angle 1.72848 ( 12) link_NAG-ASN : bond 0.00282 ( 8) link_NAG-ASN : angle 2.36801 ( 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 213 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7757 (mt-10) REVERT: A 173 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.5157 (ptp90) REVERT: A 260 TYR cc_start: 0.7589 (m-10) cc_final: 0.7236 (m-10) REVERT: A 493 HIS cc_start: 0.4674 (OUTLIER) cc_final: 0.3869 (m-70) REVERT: A 852 MET cc_start: 0.8707 (tpp) cc_final: 0.8206 (mpp) REVERT: B 156 TRP cc_start: 0.7965 (m-90) cc_final: 0.7573 (m-90) REVERT: C 38 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7767 (mt-10) REVERT: C 172 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5505 (tp) REVERT: C 230 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: C 524 ASN cc_start: 0.8201 (t0) cc_final: 0.7480 (t0) REVERT: D 156 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.7661 (m-90) outliers start: 67 outliers final: 52 residues processed: 199 average time/residue: 0.1587 time to fit residues: 49.8270 Evaluate side-chains 195 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 142 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 406 GLN B 203 GLN C 52 HIS D 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085367 restraints weight = 50139.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085548 restraints weight = 31586.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086355 restraints weight = 24154.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086707 restraints weight = 22191.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086903 restraints weight = 19588.998| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23134 Z= 0.116 Angle : 0.583 11.438 31288 Z= 0.276 Chirality : 0.044 0.506 3520 Planarity : 0.004 0.048 3806 Dihedral : 13.326 115.158 5126 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.43 % Allowed : 18.83 % Favored : 78.74 % 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: 0.36 (0.16), residues: 2636 helix: 1.46 (0.15), residues: 1224 sheet: -0.54 (0.32), residues: 266 loop : -0.90 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.009 0.001 TYR A 869 PHE 0.027 0.001 PHE C 184 TRP 0.040 0.001 TRP C 418 HIS 0.022 0.002 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00256 (23090) covalent geometry : angle 0.56124 (31162) SS BOND : bond 0.00078 ( 6) SS BOND : angle 0.73196 ( 12) hydrogen bonds : bond 0.04667 ( 998) hydrogen bonds : angle 4.17593 ( 2892) link_ALPHA1-3 : bond 0.00882 ( 6) link_ALPHA1-3 : angle 3.74066 ( 18) link_ALPHA1-6 : bond 0.00707 ( 4) link_ALPHA1-6 : angle 1.68412 ( 12) link_BETA1-2 : bond 0.00418 ( 2) link_BETA1-2 : angle 4.38966 ( 6) link_BETA1-4 : bond 0.00509 ( 14) link_BETA1-4 : angle 2.56603 ( 42) link_BETA1-6 : bond 0.00101 ( 4) link_BETA1-6 : angle 1.62504 ( 12) link_NAG-ASN : bond 0.00348 ( 8) link_NAG-ASN : angle 2.03547 ( 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 193 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7744 (mt-10) REVERT: A 173 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5199 (ptp90) REVERT: A 260 TYR cc_start: 0.7599 (m-10) cc_final: 0.7217 (m-10) REVERT: A 493 HIS cc_start: 0.4487 (OUTLIER) cc_final: 0.3739 (m-70) REVERT: B 156 TRP cc_start: 0.7876 (m-90) cc_final: 0.7621 (m-90) REVERT: C 38 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7670 (mt-10) REVERT: C 172 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5483 (tp) REVERT: C 524 ASN cc_start: 0.8234 (t0) cc_final: 0.7515 (t0) REVERT: D 156 TRP cc_start: 0.7828 (OUTLIER) cc_final: 0.7568 (m-90) outliers start: 55 outliers final: 45 residues processed: 181 average time/residue: 0.1631 time to fit residues: 46.2126 Evaluate side-chains 179 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 76 optimal weight: 0.0470 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 85 optimal weight: 0.0370 overall best weight: 3.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.111324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083146 restraints weight = 50365.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083286 restraints weight = 33008.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084277 restraints weight = 24205.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084651 restraints weight = 21783.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084689 restraints weight = 20464.233| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23134 Z= 0.194 Angle : 0.646 11.534 31288 Z= 0.307 Chirality : 0.046 0.519 3520 Planarity : 0.004 0.046 3806 Dihedral : 13.416 118.973 5126 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.34 % Allowed : 18.83 % Favored : 78.82 % 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: 0.24 (0.16), residues: 2636 helix: 1.36 (0.15), residues: 1212 sheet: -0.63 (0.32), residues: 266 loop : -0.92 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 61 TYR 0.015 0.002 TYR A 869 PHE 0.025 0.002 PHE C 184 TRP 0.024 0.002 TRP C 418 HIS 0.013 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00467 (23090) covalent geometry : angle 0.62586 (31162) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.85729 ( 12) hydrogen bonds : bond 0.05283 ( 998) hydrogen bonds : angle 4.34796 ( 2892) link_ALPHA1-3 : bond 0.00837 ( 6) link_ALPHA1-3 : angle 3.83672 ( 18) link_ALPHA1-6 : bond 0.00826 ( 4) link_ALPHA1-6 : angle 1.75342 ( 12) link_BETA1-2 : bond 0.00316 ( 2) link_BETA1-2 : angle 4.25849 ( 6) link_BETA1-4 : bond 0.00546 ( 14) link_BETA1-4 : angle 2.57909 ( 42) link_BETA1-6 : bond 0.00150 ( 4) link_BETA1-6 : angle 1.68235 ( 12) link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.25674 ( 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 186 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7774 (mt-10) REVERT: A 173 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.5011 (ptp90) REVERT: A 260 TYR cc_start: 0.7621 (m-10) cc_final: 0.7279 (m-10) REVERT: A 493 HIS cc_start: 0.4736 (OUTLIER) cc_final: 0.3948 (m-70) REVERT: A 852 MET cc_start: 0.8734 (tpp) cc_final: 0.8191 (mpp) REVERT: B 156 TRP cc_start: 0.7959 (m-90) cc_final: 0.7637 (m-90) REVERT: C 38 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7719 (mt-10) REVERT: C 172 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5750 (tp) REVERT: C 524 ASN cc_start: 0.8202 (t0) cc_final: 0.7516 (t0) REVERT: D 156 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.7711 (m-90) outliers start: 53 outliers final: 44 residues processed: 176 average time/residue: 0.1608 time to fit residues: 44.6521 Evaluate side-chains 178 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN C 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084166 restraints weight = 50064.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084482 restraints weight = 34740.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085242 restraints weight = 26065.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085775 restraints weight = 22153.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085786 restraints weight = 21285.061| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23134 Z= 0.155 Angle : 0.618 11.589 31288 Z= 0.292 Chirality : 0.044 0.510 3520 Planarity : 0.004 0.044 3806 Dihedral : 13.208 115.262 5124 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.30 % Allowed : 19.23 % Favored : 78.47 % 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: 0.32 (0.16), residues: 2636 helix: 1.38 (0.15), residues: 1224 sheet: -0.59 (0.32), residues: 264 loop : -0.84 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 350 TYR 0.012 0.001 TYR A 869 PHE 0.025 0.001 PHE C 184 TRP 0.041 0.002 TRP C 418 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00370 (23090) covalent geometry : angle 0.59788 (31162) SS BOND : bond 0.00070 ( 6) SS BOND : angle 0.88688 ( 12) hydrogen bonds : bond 0.04907 ( 998) hydrogen bonds : angle 4.24202 ( 2892) link_ALPHA1-3 : bond 0.00747 ( 6) link_ALPHA1-3 : angle 3.75424 ( 18) link_ALPHA1-6 : bond 0.00719 ( 4) link_ALPHA1-6 : angle 1.77501 ( 12) link_BETA1-2 : bond 0.00352 ( 2) link_BETA1-2 : angle 4.31127 ( 6) link_BETA1-4 : bond 0.00500 ( 14) link_BETA1-4 : angle 2.44489 ( 42) link_BETA1-6 : bond 0.00100 ( 4) link_BETA1-6 : angle 1.63199 ( 12) link_NAG-ASN : bond 0.00308 ( 8) link_NAG-ASN : angle 2.10678 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3267.90 seconds wall clock time: 57 minutes 31.22 seconds (3451.22 seconds total)