Starting phenix.real_space_refine on Sat Jul 4 19:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jfz_36220/07_2026/8jfz_36220.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 4 5.21 5 S 118 5.16 5 C 14458 2.51 5 N 3496 2.21 5 O 4244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22340 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7633 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 943} Chain: "E" 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: "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': 4, 'PTRANS': 11, 'TRANS': 278} Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7633 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 943} 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 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 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 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 chiralities: 2 Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 452 Unusual residues: {' MG': 2, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 508 Unusual residues: {' MG': 2, 'CLR': 3, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: D, G, K, L, M, N Time building chain proxies: 5.36, per 1000 atoms: 0.24 Number of scatterers: 22340 At special positions: 0 Unit cell: (200.136, 179.692, 100.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 20 15.00 Mg 4 11.99 O 4244 8.00 N 3496 7.00 C 14458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" CE1 PHE D 65 " - pdb=" CE1 PHE D 65 " distance=0.00 Simple disulfide: pdb=" CD2 TYR D 83 " - pdb=" CD2 TYR D 83 " distance=0.00 Simple disulfide: pdb=" N ASN D 114 " - pdb=" N ASN D 114 " distance=0.00 Simple disulfide: pdb=" CD LYS D 180 " - pdb=" CD LYS D 180 " distance=0.00 Simple disulfide: pdb=" CA ALA D 216 " - pdb=" CA ALA D 216 " distance=0.00 Simple disulfide: pdb=" CA VAL D 299 " - pdb=" CA VAL D 299 " distance=0.00 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 D 114 " " NAG H 1 " - " ASN D 159 " " NAG I 1 " - " ASN D 194 " " NAG J 1 " - " ASN D 267 " " NAG K 1 " - " ASN B 114 " " NAG L 1 " - " ASN B 159 " " NAG M 1 " - " ASN B 194 " " NAG N 1 " - " ASN B 267 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 813.4 milliseconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 20 sheets defined 49.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'D' and resid 29 through 62 removed outlier: 3.722A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.721A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.929A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.377A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.739A 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: 4.212A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.537A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 121 removed outlier: 3.713A pdb=" N LEU C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 161 removed outlier: 3.646A pdb=" N THR C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) 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 275 removed outlier: 3.503A pdb=" N ARG C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 313 Processing helix chain 'C' and resid 316 through 332 removed outlier: 3.512A pdb=" N VAL C 321 " --> pdb=" O TRP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 360 through 369 removed outlier: 4.087A pdb=" N VAL C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.606A pdb=" N ALA C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.542A pdb=" N MET C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 517 Processing helix chain 'C' and resid 531 through 548 removed outlier: 3.512A pdb=" N LEU C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 620 through 632 Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 667 through 673 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 696 No H-bonds generated for 'chain 'C' and resid 694 through 696' Processing helix chain 'C' and resid 697 through 709 removed outlier: 3.542A pdb=" N GLN C 708 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 709 " --> pdb=" O CYS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 755 through 782 removed outlier: 3.550A pdb=" N LEU C 767 " --> pdb=" O GLU C 763 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 768 " --> pdb=" O GLU C 764 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 781 " --> pdb=" O ALA C 777 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 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 removed outlier: 3.630A pdb=" N ILE C 820 " --> pdb=" O MET C 816 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 822 " --> pdb=" O PRO C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 832 removed outlier: 4.281A pdb=" N MET C 832 " --> pdb=" O SER C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.700A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 877 removed outlier: 3.980A pdb=" N ILE C 860 " --> pdb=" O GLN C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 884 removed outlier: 3.657A pdb=" N LEU C 883 " --> pdb=" O LEU C 879 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 879 through 884' Processing helix chain 'C' and resid 885 through 891 removed outlier: 4.676A pdb=" N ARG C 889 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 938 removed outlier: 3.595A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 938 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.642A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 989 removed outlier: 4.005A pdb=" N TRP C 988 " --> pdb=" O LYS C 984 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 984 through 989' Processing helix chain 'C' and resid 991 through 1012 Processing helix chain 'C' and resid 1015 through 1022 removed outlier: 3.576A pdb=" N TYR C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 15 through 40 Processing helix chain 'B' and resid 29 through 62 removed outlier: 3.721A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.721A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.929A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.377A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.740A 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: 4.212A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.537A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.713A pdb=" N LEU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 161 removed outlier: 3.646A pdb=" N THR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) 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 275 removed outlier: 3.504A pdb=" N ARG A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.512A pdb=" N VAL A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 360 through 369 removed outlier: 4.088A pdb=" N VAL A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.606A pdb=" N ALA A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.541A pdb=" N MET A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 531 through 548 removed outlier: 3.511A pdb=" N LEU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.542A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 709 " --> pdb=" O CYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 755 through 782 removed outlier: 3.549A pdb=" N LEU A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 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 removed outlier: 3.630A pdb=" N ILE A 820 " --> pdb=" O MET A 816 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 4.281A pdb=" N MET A 832 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.700A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.980A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.656A pdb=" N LEU A 883 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 884' Processing helix chain 'A' and resid 885 through 891 removed outlier: 4.677A pdb=" N ARG A 889 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 938 removed outlier: 3.595A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.642A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 4.005A pdb=" N TRP A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 984 through 989' Processing helix chain 'A' and resid 991 through 1012 Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.575A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.627A pdb=" N ASP D 19 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 78 through 81 Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 92 Processing sheet with id=AA4, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'C' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS C 249 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 214 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR C 253 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG C 255 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C 208 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL C 257 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 206 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 259 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ARG C 204 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS C 211 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS C 249 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 214 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR C 253 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG C 255 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C 208 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL C 257 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 206 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 259 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ARG C 204 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 356 through 358 removed outlier: 5.870A pdb=" N GLY C 731 " --> pdb=" O MET C 748 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 750 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 733 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP C 376 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA C 590 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET C 391 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 588 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE C 393 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL C 586 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 478 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA C 590 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET C 391 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 588 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE C 393 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL C 586 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N CYS C 518 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 585 " --> pdb=" O CYS C 518 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 520 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY C 587 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N LEU C 522 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 12.519A pdb=" N MET C 589 " --> pdb=" O LEU C 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AB2, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.628A pdb=" N ASP B 19 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 24 " --> pdb=" O ASP B 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 78 through 81 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 92 Processing sheet with id=AB5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB6, first strand: chain 'A' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS A 249 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 214 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR A 253 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 210 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG A 255 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA A 208 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 257 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 206 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 259 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG A 204 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS A 249 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 214 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR A 253 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 210 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG A 255 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ALA A 208 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 257 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 206 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 259 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG A 204 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 356 through 358 removed outlier: 5.870A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 376 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N CYS A 518 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 585 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY A 587 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 12.519A pdb=" N MET A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 898 through 899 1044 hydrogen bonds defined for protein. 2988 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: 3.92 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6670 1.34 - 1.46: 4950 1.46 - 1.58: 10925 1.58 - 1.71: 51 1.71 - 1.83: 172 Bond restraints: 22768 Sorted by residual: bond pdb=" C39 PCW A1111 " pdb=" C40 PCW A1111 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C39 PCW C1109 " pdb=" C40 PCW C1109 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C39 PCW C1106 " pdb=" C40 PCW C1106 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C39 PCW A1108 " pdb=" C40 PCW A1108 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C39 PCW C1107 " pdb=" C40 PCW C1107 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 22763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 27888 2.43 - 4.86: 2208 4.86 - 7.30: 466 7.30 - 9.73: 126 9.73 - 12.16: 42 Bond angle restraints: 30730 Sorted by residual: angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 111.03 121.59 -10.56 1.11e+00 8.12e-01 9.05e+01 angle pdb=" N LYS B 158 " pdb=" CA LYS B 158 " pdb=" C LYS B 158 " ideal model delta sigma weight residual 111.03 121.51 -10.48 1.11e+00 8.12e-01 8.91e+01 angle pdb=" N TYR A 970 " pdb=" CA TYR A 970 " pdb=" C TYR A 970 " ideal model delta sigma weight residual 112.23 120.57 -8.34 1.26e+00 6.30e-01 4.38e+01 angle pdb=" N TYR C 970 " pdb=" CA TYR C 970 " pdb=" C TYR C 970 " ideal model delta sigma weight residual 112.23 120.57 -8.34 1.26e+00 6.30e-01 4.38e+01 angle pdb=" N THR A1021 " pdb=" CA THR A1021 " pdb=" C THR A1021 " ideal model delta sigma weight residual 112.23 120.52 -8.29 1.26e+00 6.30e-01 4.33e+01 ... (remaining 30725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.66: 12580 30.66 - 61.31: 690 61.31 - 91.97: 46 91.97 - 122.62: 22 122.62 - 153.28: 8 Dihedral angle restraints: 13346 sinusoidal: 5726 harmonic: 7620 Sorted by residual: dihedral pdb=" C33 PCW A1110 " pdb=" C31 PCW A1110 " pdb=" C32 PCW A1110 " pdb=" O2 PCW A1110 " ideal model delta sinusoidal sigma weight residual 191.83 38.55 153.28 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C33 PCW C1108 " pdb=" C31 PCW C1108 " pdb=" C32 PCW C1108 " pdb=" O2 PCW C1108 " ideal model delta sinusoidal sigma weight residual 191.83 38.57 153.26 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" N PCW G1302 " pdb=" C4 PCW G1302 " pdb=" C5 PCW G1302 " pdb=" O4P PCW G1302 " ideal model delta sinusoidal sigma weight residual 293.34 150.31 143.03 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 13343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2734 0.078 - 0.156: 601 0.156 - 0.234: 99 0.234 - 0.312: 43 0.312 - 0.389: 15 Chirality restraints: 3492 Sorted by residual: 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 5.40e+01 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 5.37e+01 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.54e+01 ... (remaining 3489 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " -0.082 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO A 283 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " 0.082 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO C 283 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 917 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C THR C 917 " -0.077 2.00e-02 2.50e+03 pdb=" O THR C 917 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS C 918 " 0.026 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 250 2.60 - 3.18: 19197 3.18 - 3.75: 32129 3.75 - 4.33: 46325 4.33 - 4.90: 75494 Nonbonded interactions: 173395 Sorted by model distance: nonbonded pdb=" SG CYS D 160 " pdb=" SG CYS D 176 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 160 " pdb=" SG CYS B 176 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS D 215 " pdb=" SG CYS D 278 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 215 " pdb=" SG CYS B 278 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 127 " pdb=" SG CYS D 150 " model vdw 2.032 3.760 ... (remaining 173390 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 1101 or resid 1104 through 1110)) selection = (chain 'C' and (resid 37 through 1101 or (resid 1104 through 1105 and (name N or \ name C1 or name C11 or name C12 or name C2 or name C3 or name C31 or name C32 o \ r name C4 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or resid 1106 through 1110)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } 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: 0.930 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.570 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.207 22806 Z= 0.558 Angle : 1.573 17.454 30850 Z= 0.827 Chirality : 0.075 0.389 3492 Planarity : 0.013 0.127 3774 Dihedral : 17.923 153.281 8446 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 7.50 % Allowed : 9.19 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: -1.79 (0.15), residues: 2630 helix: -0.05 (0.15), residues: 1130 sheet: -1.65 (0.25), residues: 326 loop : -2.18 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 893 TYR 0.028 0.003 TYR A 970 PHE 0.036 0.004 PHE C 100 TRP 0.026 0.003 TRP D 156 HIS 0.010 0.003 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.01118 / 0.56 (22768) covalent geometry : angle 1.55408 / 0.82 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.15870 / 10.36 ( 1002) hydrogen bonds : angle 7.08693 / 5.14 ( 2988) link_ALPHA1-3 : bond 0.00816 / 0.56 ( 6) link_ALPHA1-3 : angle 3.04808 / 1.46 ( 18) link_ALPHA1-6 : bond 0.00743 / 0.50 ( 4) link_ALPHA1-6 : angle 1.28238 / 0.66 ( 12) link_BETA1-2 : bond 0.00979 / 0.58 ( 2) link_BETA1-2 : angle 5.34523 / 2.58 ( 6) link_BETA1-4 : bond 0.00862 / 0.59 ( 14) link_BETA1-4 : angle 5.98596 / 3.66 ( 42) link_BETA1-6 : bond 0.00273 / 0.16 ( 4) link_BETA1-6 : angle 1.04426 / 0.50 ( 12) link_NAG-ASN : bond 0.01413 / 0.95 ( 8) link_NAG-ASN : angle 3.40218 / 2.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 444 time to evaluate : 0.746 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: D 17 LEU cc_start: 0.7965 (tp) cc_final: 0.7618 (tt) REVERT: C 168 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7614 (mm-40) REVERT: C 534 MET cc_start: 0.5596 (mmp) cc_final: 0.5362 (mmm) REVERT: C 794 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 849 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 949 MET cc_start: 0.9004 (tpt) cc_final: 0.8751 (mmt) REVERT: B 20 SER cc_start: 0.6838 (OUTLIER) cc_final: 0.6513 (m) REVERT: B 56 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: B 156 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: A 155 SER cc_start: 0.8062 (m) cc_final: 0.7744 (p) REVERT: A 199 ILE cc_start: 0.7917 (mm) cc_final: 0.7670 (mm) REVERT: A 224 PRO cc_start: 0.6319 (Cg_exo) cc_final: 0.5997 (Cg_endo) REVERT: A 357 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 534 MET cc_start: 0.4846 (mmp) cc_final: 0.4376 (mmm) REVERT: A 543 LEU cc_start: 0.7226 (mt) cc_final: 0.6953 (tp) REVERT: A 734 MET cc_start: 0.8825 (mmp) cc_final: 0.8600 (mmm) REVERT: A 794 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 849 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 911 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.5327 (mtp-110) REVERT: A 1023 TYR cc_start: 0.8608 (p90) cc_final: 0.8268 (p90) outliers start: 169 outliers final: 21 residues processed: 573 average time/residue: 0.1601 time to fit residues: 134.5875 Evaluate side-chains 214 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 HIS D 258 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 235 ASN C 248 ASN C 396 GLN C 434 GLN C 439 ASN C 474 ASN C 483 ASN C 489 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 GLN C 577 ASN ** C 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN C 656 ASN C 666 HIS C 744 GLN C 783 ASN C 904 GLN C 905 GLN C 910 GLN C 919 HIS B 107 HIS B 258 GLN A 53 ASN A 129 ASN A 167 GLN A 215 ASN A 235 ASN A 248 ASN A 396 GLN A 405 ASN A 434 GLN A 439 ASN A 483 ASN A 539 GLN A 654 GLN A 656 ASN A 666 HIS A 708 GLN A 783 ASN A 905 GLN A 910 GLN A 919 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.149657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111563 restraints weight = 39289.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108330 restraints weight = 37094.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109871 restraints weight = 35756.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109988 restraints weight = 24198.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112372 restraints weight = 20920.216| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22806 Z= 0.182 Angle : 0.725 10.756 30850 Z= 0.359 Chirality : 0.047 0.437 3492 Planarity : 0.008 0.075 3774 Dihedral : 15.171 147.847 3575 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 13.19 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: -0.11 (0.16), residues: 2630 helix: 1.33 (0.15), residues: 1150 sheet: -1.04 (0.28), residues: 264 loop : -1.24 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 240 TYR 0.016 0.002 TYR D 40 PHE 0.024 0.002 PHE A 393 TRP 0.019 0.001 TRP C 890 HIS 0.012 0.002 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (22768) covalent geometry : angle 0.70455 / 0.35 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.06339 / 4.09 ( 1002) hydrogen bonds : angle 4.84621 / 3.53 ( 2988) link_ALPHA1-3 : bond 0.00780 / 0.55 ( 6) link_ALPHA1-3 : angle 2.92957 / 1.46 ( 18) link_ALPHA1-6 : bond 0.00664 / 0.47 ( 4) link_ALPHA1-6 : angle 1.44566 / 0.76 ( 12) link_BETA1-2 : bond 0.00988 / 0.58 ( 2) link_BETA1-2 : angle 4.25717 / 2.05 ( 6) link_BETA1-4 : bond 0.00861 / 0.57 ( 14) link_BETA1-4 : angle 3.50183 / 2.15 ( 42) link_BETA1-6 : bond 0.00187 / 0.15 ( 4) link_BETA1-6 : angle 1.58403 / 0.88 ( 12) link_NAG-ASN : bond 0.00630 / 0.43 ( 8) link_NAG-ASN : angle 2.35862 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.2600 (pmm) cc_final: 0.1781 (ppp) REVERT: C 52 HIS cc_start: 0.3312 (t70) cc_final: 0.3111 (t70) REVERT: C 238 GLU cc_start: 0.6674 (tp30) cc_final: 0.6341 (mm-30) REVERT: C 395 ASN cc_start: 0.5618 (t0) cc_final: 0.5344 (t0) REVERT: C 470 MET cc_start: 0.6986 (mmm) cc_final: 0.6583 (mmt) REVERT: C 734 MET cc_start: 0.8675 (mmt) cc_final: 0.8458 (mmt) REVERT: C 911 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7792 (ptt180) REVERT: E 13 THR cc_start: 0.8528 (m) cc_final: 0.8229 (p) REVERT: B 159 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 180 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (ttpp) REVERT: A 55 TYR cc_start: 0.4136 (m-80) cc_final: 0.3772 (m-80) REVERT: A 199 ILE cc_start: 0.8169 (mm) cc_final: 0.7889 (mm) REVERT: A 202 ASP cc_start: 0.5490 (m-30) cc_final: 0.5282 (m-30) REVERT: A 206 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6488 (pt) REVERT: A 395 ASN cc_start: 0.4831 (t0) cc_final: 0.4468 (t0) REVERT: A 534 MET cc_start: 0.4881 (mmp) cc_final: 0.4235 (mmm) REVERT: A 734 MET cc_start: 0.8856 (mmp) cc_final: 0.8625 (mmm) REVERT: A 911 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7435 (ptp90) REVERT: G 10 GLU cc_start: 0.7387 (tp30) cc_final: 0.7149 (tp30) outliers start: 78 outliers final: 38 residues processed: 260 average time/residue: 0.1513 time to fit residues: 60.9995 Evaluate side-chains 199 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 911 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 257 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 HIS B 264 GLN B 271 ASN A 209 HIS A 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.147132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108602 restraints weight = 39132.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105099 restraints weight = 37869.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106617 restraints weight = 37535.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106595 restraints weight = 25225.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109081 restraints weight = 21293.973| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22806 Z= 0.158 Angle : 0.618 10.436 30850 Z= 0.304 Chirality : 0.043 0.391 3492 Planarity : 0.005 0.056 3774 Dihedral : 13.536 150.450 3539 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.06 % Allowed : 14.03 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.49 (0.16), residues: 2630 helix: 1.71 (0.15), residues: 1168 sheet: -0.64 (0.28), residues: 276 loop : -0.85 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 173 TYR 0.016 0.001 TYR D 206 PHE 0.019 0.001 PHE C 793 TRP 0.018 0.001 TRP B 156 HIS 0.011 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (22768) covalent geometry : angle 0.59943 / 0.30 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05537 / 3.57 ( 1002) hydrogen bonds : angle 4.47828 / 3.26 ( 2988) link_ALPHA1-3 : bond 0.00838 / 0.59 ( 6) link_ALPHA1-3 : angle 2.54639 / 1.31 ( 18) link_ALPHA1-6 : bond 0.00680 / 0.48 ( 4) link_ALPHA1-6 : angle 1.38874 / 0.76 ( 12) link_BETA1-2 : bond 0.00727 / 0.43 ( 2) link_BETA1-2 : angle 3.71758 / 1.79 ( 6) link_BETA1-4 : bond 0.00739 / 0.49 ( 14) link_BETA1-4 : angle 3.13502 / 1.88 ( 42) link_BETA1-6 : bond 0.00141 / 0.08 ( 4) link_BETA1-6 : angle 1.29565 / 0.71 ( 12) link_NAG-ASN : bond 0.00492 / 0.35 ( 8) link_NAG-ASN : angle 1.84493 / 1.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 170 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 200 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7417 (tp30) REVERT: C 41 MET cc_start: 0.2631 (pmm) cc_final: 0.1324 (tmm) REVERT: C 52 HIS cc_start: 0.3509 (t70) cc_final: 0.3236 (t70) REVERT: C 346 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8744 (tp) REVERT: C 391 MET cc_start: 0.5586 (mpp) cc_final: 0.5254 (mpp) REVERT: C 395 ASN cc_start: 0.5507 (t0) cc_final: 0.5293 (t0) REVERT: C 470 MET cc_start: 0.6765 (mmm) cc_final: 0.6554 (mmt) REVERT: C 534 MET cc_start: 0.5011 (mmm) cc_final: 0.4515 (mmm) REVERT: C 553 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7491 (pt) REVERT: C 911 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7910 (ptt90) REVERT: C 1006 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7821 (mtt-85) REVERT: E 10 GLU cc_start: 0.7373 (tp30) cc_final: 0.6915 (tp30) REVERT: E 13 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 199 ILE cc_start: 0.8301 (mm) cc_final: 0.8050 (mm) REVERT: A 202 ASP cc_start: 0.5571 (m-30) cc_final: 0.5352 (m-30) REVERT: A 395 ASN cc_start: 0.4960 (t0) cc_final: 0.4694 (t0) REVERT: A 489 GLN cc_start: 0.3741 (tp40) cc_final: 0.3414 (tp40) REVERT: A 534 MET cc_start: 0.4916 (mmp) cc_final: 0.4306 (mmm) REVERT: A 780 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 847 GLU cc_start: 0.7567 (pp20) cc_final: 0.7353 (pp20) REVERT: A 852 MET cc_start: 0.7589 (tpp) cc_final: 0.7381 (tpt) REVERT: A 911 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8017 (ptt180) REVERT: G 14 TYR cc_start: 0.8610 (t80) cc_final: 0.8368 (t80) outliers start: 69 outliers final: 38 residues processed: 227 average time/residue: 0.1457 time to fit residues: 51.5842 Evaluate side-chains 188 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 151 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108655 restraints weight = 38855.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104873 restraints weight = 37453.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106705 restraints weight = 35525.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106461 restraints weight = 24037.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109054 restraints weight = 20605.122| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22806 Z= 0.132 Angle : 0.567 9.322 30850 Z= 0.277 Chirality : 0.042 0.398 3492 Planarity : 0.005 0.051 3774 Dihedral : 12.708 150.260 3537 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.49 % Allowed : 14.52 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2630 helix: 1.82 (0.15), residues: 1170 sheet: -0.35 (0.29), residues: 270 loop : -0.77 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.013 0.001 TYR A 869 PHE 0.020 0.001 PHE B 25 TRP 0.010 0.001 TRP B 156 HIS 0.019 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (22768) covalent geometry : angle 0.54885 / 0.27 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04975 / 3.19 ( 1002) hydrogen bonds : angle 4.31931 / 3.16 ( 2988) link_ALPHA1-3 : bond 0.00706 / 0.49 ( 6) link_ALPHA1-3 : angle 2.56102 / 1.31 ( 18) link_ALPHA1-6 : bond 0.00649 / 0.46 ( 4) link_ALPHA1-6 : angle 1.38118 / 0.76 ( 12) link_BETA1-2 : bond 0.00635 / 0.38 ( 2) link_BETA1-2 : angle 3.85359 / 1.85 ( 6) link_BETA1-4 : bond 0.00647 / 0.42 ( 14) link_BETA1-4 : angle 2.82166 / 1.70 ( 42) link_BETA1-6 : bond 0.00075 / 0.04 ( 4) link_BETA1-6 : angle 1.37697 / 0.76 ( 12) link_NAG-ASN : bond 0.00515 / 0.37 ( 8) link_NAG-ASN : angle 1.72963 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8503 (t0) REVERT: D 160 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7891 (m) REVERT: D 200 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 41 MET cc_start: 0.2749 (pmm) cc_final: 0.1385 (tmm) REVERT: C 52 HIS cc_start: 0.3559 (t70) cc_final: 0.3240 (t70) REVERT: C 90 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6248 (mt) REVERT: C 255 ARG cc_start: 0.4531 (OUTLIER) cc_final: 0.3924 (mmm-85) REVERT: C 534 MET cc_start: 0.5049 (mmm) cc_final: 0.4793 (mmm) REVERT: C 553 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7593 (pt) REVERT: C 911 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: C 1006 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7771 (mtt-85) REVERT: E 10 GLU cc_start: 0.7318 (tp30) cc_final: 0.7079 (tp30) REVERT: E 13 THR cc_start: 0.8541 (m) cc_final: 0.8314 (p) REVERT: A 70 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6683 (tm-30) REVERT: A 199 ILE cc_start: 0.8393 (mm) cc_final: 0.8151 (mm) REVERT: A 202 ASP cc_start: 0.5596 (m-30) cc_final: 0.5349 (m-30) REVERT: A 395 ASN cc_start: 0.5094 (t0) cc_final: 0.4828 (t0) REVERT: A 534 MET cc_start: 0.4873 (mmp) cc_final: 0.4223 (mmm) REVERT: A 699 LEU cc_start: 0.8267 (tp) cc_final: 0.7757 (tp) REVERT: A 911 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7962 (ptt180) REVERT: G 14 TYR cc_start: 0.8723 (t80) cc_final: 0.8507 (t80) outliers start: 56 outliers final: 34 residues processed: 204 average time/residue: 0.1441 time to fit residues: 46.8435 Evaluate side-chains 184 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 117 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101459 restraints weight = 39149.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097463 restraints weight = 43695.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099347 restraints weight = 44172.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099165 restraints weight = 30734.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100359 restraints weight = 25049.234| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22806 Z= 0.214 Angle : 0.647 9.531 30850 Z= 0.318 Chirality : 0.045 0.389 3492 Planarity : 0.005 0.049 3774 Dihedral : 12.738 153.491 3535 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.00 % Allowed : 13.59 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.56 (0.16), residues: 2630 helix: 1.59 (0.15), residues: 1162 sheet: -0.23 (0.30), residues: 268 loop : -0.68 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 223 TYR 0.027 0.002 TYR D 248 PHE 0.027 0.002 PHE C 793 TRP 0.014 0.001 TRP C 105 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 (22768) covalent geometry : angle 0.63205 / 0.31 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05989 / 3.86 ( 1002) hydrogen bonds : angle 4.44895 / 3.25 ( 2988) link_ALPHA1-3 : bond 0.00576 / 0.39 ( 6) link_ALPHA1-3 : angle 2.50093 / 1.29 ( 18) link_ALPHA1-6 : bond 0.00600 / 0.42 ( 4) link_ALPHA1-6 : angle 1.37354 / 0.75 ( 12) link_BETA1-2 : bond 0.00732 / 0.43 ( 2) link_BETA1-2 : angle 3.61584 / 1.74 ( 6) link_BETA1-4 : bond 0.00546 / 0.36 ( 14) link_BETA1-4 : angle 2.85501 / 1.71 ( 42) link_BETA1-6 : bond 0.00199 / 0.12 ( 4) link_BETA1-6 : angle 1.44382 / 0.76 ( 12) link_NAG-ASN : bond 0.00363 / 0.25 ( 8) link_NAG-ASN : angle 1.78547 / 1.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 166 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8649 (t0) REVERT: D 160 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7922 (m) REVERT: D 200 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7582 (tp30) REVERT: D 270 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 41 MET cc_start: 0.2984 (pmm) cc_final: 0.1137 (tmm) REVERT: C 52 HIS cc_start: 0.3713 (t70) cc_final: 0.3373 (t70) REVERT: C 90 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6336 (mt) REVERT: C 255 ARG cc_start: 0.4382 (OUTLIER) cc_final: 0.4016 (mmm-85) REVERT: C 520 THR cc_start: 0.5638 (OUTLIER) cc_final: 0.5193 (p) REVERT: C 535 LYS cc_start: 0.6268 (mttt) cc_final: 0.5551 (ttpp) REVERT: C 553 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7605 (pt) REVERT: C 780 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 911 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8110 (ptt180) REVERT: E 13 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (p) REVERT: B 222 ASP cc_start: 0.7195 (m-30) cc_final: 0.6984 (m-30) REVERT: A 70 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 244 PHE cc_start: 0.7016 (m-80) cc_final: 0.6643 (m-80) REVERT: A 534 MET cc_start: 0.4845 (mmp) cc_final: 0.4179 (mmm) REVERT: A 699 LEU cc_start: 0.8044 (tp) cc_final: 0.7838 (tp) REVERT: A 780 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 895 ILE cc_start: 0.8666 (mt) cc_final: 0.8419 (tt) REVERT: A 911 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8093 (ptt180) outliers start: 90 outliers final: 53 residues processed: 243 average time/residue: 0.1465 time to fit residues: 55.6939 Evaluate side-chains 204 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 200 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 211 optimal weight: 20.0000 chunk 132 optimal weight: 0.1980 chunk 202 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102153 restraints weight = 39010.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098223 restraints weight = 33273.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099418 restraints weight = 35464.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099740 restraints weight = 25694.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101023 restraints weight = 21970.850| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22806 Z= 0.138 Angle : 0.564 10.446 30850 Z= 0.277 Chirality : 0.042 0.393 3492 Planarity : 0.004 0.051 3774 Dihedral : 12.340 152.899 3534 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.11 % Allowed : 15.23 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.72 (0.16), residues: 2630 helix: 1.72 (0.16), residues: 1170 sheet: -0.24 (0.30), residues: 274 loop : -0.58 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.018 0.001 TYR A 869 PHE 0.016 0.001 PHE B 25 TRP 0.010 0.001 TRP B 156 HIS 0.044 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22768) covalent geometry : angle 0.54796 / 0.27 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05094 / 3.27 ( 1002) hydrogen bonds : angle 4.25394 / 3.10 ( 2988) link_ALPHA1-3 : bond 0.00626 / 0.43 ( 6) link_ALPHA1-3 : angle 2.48859 / 1.27 ( 18) link_ALPHA1-6 : bond 0.00614 / 0.43 ( 4) link_ALPHA1-6 : angle 1.31833 / 0.73 ( 12) link_BETA1-2 : bond 0.00637 / 0.38 ( 2) link_BETA1-2 : angle 3.71103 / 1.78 ( 6) link_BETA1-4 : bond 0.00549 / 0.36 ( 14) link_BETA1-4 : angle 2.64094 / 1.57 ( 42) link_BETA1-6 : bond 0.00181 / 0.12 ( 4) link_BETA1-6 : angle 1.44081 / 0.78 ( 12) link_NAG-ASN : bond 0.00457 / 0.32 ( 8) link_NAG-ASN : angle 1.61176 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8645 (t0) REVERT: D 160 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7916 (m) REVERT: D 200 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7557 (tp30) REVERT: C 52 HIS cc_start: 0.4052 (t70) cc_final: 0.3731 (t70) REVERT: C 309 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8968 (tt) REVERT: C 520 THR cc_start: 0.5721 (OUTLIER) cc_final: 0.5210 (p) REVERT: C 780 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8637 (mp) REVERT: C 911 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8163 (ptt180) REVERT: E 13 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8550 (p) REVERT: B 159 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8480 (t0) REVERT: A 365 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: A 507 MET cc_start: 0.4194 (mmm) cc_final: 0.3835 (mmm) REVERT: A 534 MET cc_start: 0.4805 (mmp) cc_final: 0.4120 (mmm) REVERT: A 699 LEU cc_start: 0.7956 (tp) cc_final: 0.7756 (tp) REVERT: A 780 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8682 (mp) REVERT: A 911 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7866 (ptt-90) outliers start: 70 outliers final: 42 residues processed: 218 average time/residue: 0.1503 time to fit residues: 51.6116 Evaluate side-chains 190 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 195 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101876 restraints weight = 39156.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097216 restraints weight = 45831.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098711 restraints weight = 41877.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099668 restraints weight = 26607.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100398 restraints weight = 24236.943| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22806 Z= 0.182 Angle : 0.608 11.019 30850 Z= 0.299 Chirality : 0.043 0.385 3492 Planarity : 0.005 0.046 3774 Dihedral : 12.322 154.274 3534 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.24 % Allowed : 15.50 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.65 (0.16), residues: 2630 helix: 1.61 (0.15), residues: 1166 sheet: -0.16 (0.30), residues: 272 loop : -0.58 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 67 TYR 0.021 0.002 TYR D 248 PHE 0.022 0.002 PHE A 793 TRP 0.008 0.001 TRP C 105 HIS 0.009 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (22768) covalent geometry : angle 0.59318 / 0.30 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05551 / 3.57 ( 1002) hydrogen bonds : angle 4.30414 / 3.13 ( 2988) link_ALPHA1-3 : bond 0.00594 / 0.41 ( 6) link_ALPHA1-3 : angle 2.42557 / 1.25 ( 18) link_ALPHA1-6 : bond 0.00602 / 0.42 ( 4) link_ALPHA1-6 : angle 1.30417 / 0.72 ( 12) link_BETA1-2 : bond 0.00684 / 0.41 ( 2) link_BETA1-2 : angle 3.58600 / 1.72 ( 6) link_BETA1-4 : bond 0.00514 / 0.33 ( 14) link_BETA1-4 : angle 2.65258 / 1.57 ( 42) link_BETA1-6 : bond 0.00161 / 0.13 ( 4) link_BETA1-6 : angle 1.49593 / 0.80 ( 12) link_NAG-ASN : bond 0.00445 / 0.33 ( 8) link_NAG-ASN : angle 1.66495 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 156 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8679 (t0) REVERT: D 200 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7494 (tp30) REVERT: D 270 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: C 52 HIS cc_start: 0.3671 (t70) cc_final: 0.3315 (t70) REVERT: C 90 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6362 (mt) REVERT: C 155 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7491 (p) REVERT: C 309 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8995 (tt) REVERT: C 520 THR cc_start: 0.5551 (OUTLIER) cc_final: 0.5043 (p) REVERT: C 535 LYS cc_start: 0.6088 (mttt) cc_final: 0.5389 (ttpp) REVERT: C 615 MET cc_start: 0.7978 (tpp) cc_final: 0.7742 (tpp) REVERT: C 780 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8638 (mp) REVERT: C 911 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8159 (ptt180) REVERT: E 10 GLU cc_start: 0.7301 (tp30) cc_final: 0.7022 (tp30) REVERT: E 13 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 215 ASN cc_start: 0.6161 (m-40) cc_final: 0.5693 (p0) REVERT: A 309 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8867 (tt) REVERT: A 507 MET cc_start: 0.3827 (mmm) cc_final: 0.3526 (mmm) REVERT: A 534 MET cc_start: 0.4755 (mmp) cc_final: 0.4079 (mmm) REVERT: A 535 LYS cc_start: 0.5548 (mttt) cc_final: 0.4921 (ttpp) REVERT: A 780 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 911 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8011 (ptt-90) outliers start: 73 outliers final: 48 residues processed: 218 average time/residue: 0.1420 time to fit residues: 49.4299 Evaluate side-chains 209 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 237 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 125 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102607 restraints weight = 39405.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098096 restraints weight = 37301.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099182 restraints weight = 35808.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100199 restraints weight = 25649.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100473 restraints weight = 23829.433| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 22806 Z= 0.110 Angle : 0.544 12.116 30850 Z= 0.265 Chirality : 0.041 0.393 3492 Planarity : 0.004 0.053 3774 Dihedral : 11.702 151.446 3533 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.13 % Allowed : 16.61 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.87 (0.16), residues: 2630 helix: 1.80 (0.16), residues: 1170 sheet: 0.06 (0.31), residues: 272 loop : -0.51 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.020 0.001 TYR C 488 PHE 0.014 0.001 PHE B 25 TRP 0.009 0.001 TRP B 156 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (22768) covalent geometry : angle 0.52517 / 0.26 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04470 / 2.87 ( 1002) hydrogen bonds : angle 4.12586 / 3.00 ( 2988) link_ALPHA1-3 : bond 0.00639 / 0.44 ( 6) link_ALPHA1-3 : angle 2.47875 / 1.27 ( 18) link_ALPHA1-6 : bond 0.00615 / 0.42 ( 4) link_ALPHA1-6 : angle 1.31032 / 0.73 ( 12) link_BETA1-2 : bond 0.00677 / 0.40 ( 2) link_BETA1-2 : angle 3.62728 / 1.74 ( 6) link_BETA1-4 : bond 0.00608 / 0.39 ( 14) link_BETA1-4 : angle 2.56073 / 1.49 ( 42) link_BETA1-6 : bond 0.00102 / 0.08 ( 4) link_BETA1-6 : angle 1.40282 / 0.77 ( 12) link_NAG-ASN : bond 0.00818 / 0.59 ( 8) link_NAG-ASN : angle 2.53914 / 2.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8620 (t0) REVERT: D 200 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7404 (tp30) REVERT: C 52 HIS cc_start: 0.4059 (t70) cc_final: 0.3710 (t70) REVERT: C 90 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.6024 (mt) REVERT: C 309 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9056 (tt) REVERT: C 520 THR cc_start: 0.5806 (OUTLIER) cc_final: 0.5291 (p) REVERT: C 535 LYS cc_start: 0.6077 (mttt) cc_final: 0.5347 (ttpp) REVERT: C 671 LYS cc_start: 0.6679 (ptpp) cc_final: 0.6434 (ptpp) REVERT: C 911 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7989 (ptt-90) REVERT: E 13 THR cc_start: 0.8792 (m) cc_final: 0.8588 (p) REVERT: B 203 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: A 215 ASN cc_start: 0.6257 (m-40) cc_final: 0.5739 (p0) REVERT: A 507 MET cc_start: 0.4480 (mmm) cc_final: 0.4185 (mmm) REVERT: A 517 ARG cc_start: 0.3685 (mtt180) cc_final: 0.2865 (ttp-170) REVERT: A 534 MET cc_start: 0.4973 (mmp) cc_final: 0.4175 (mmm) REVERT: A 535 LYS cc_start: 0.5564 (mttt) cc_final: 0.4969 (ttpp) outliers start: 48 outliers final: 28 residues processed: 208 average time/residue: 0.1440 time to fit residues: 47.7694 Evaluate side-chains 188 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 1002 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 149 optimal weight: 7.9990 chunk 178 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 52 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 overall best weight: 2.1952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.139899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101030 restraints weight = 39589.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096324 restraints weight = 39120.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097717 restraints weight = 36636.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098482 restraints weight = 25131.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098857 restraints weight = 23436.998| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22806 Z= 0.150 Angle : 0.573 12.260 30850 Z= 0.280 Chirality : 0.042 0.383 3492 Planarity : 0.004 0.051 3774 Dihedral : 11.621 151.056 3528 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.04 % Allowed : 17.01 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.81 (0.16), residues: 2630 helix: 1.72 (0.16), residues: 1170 sheet: 0.10 (0.31), residues: 268 loop : -0.52 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.018 0.001 TYR A 488 PHE 0.018 0.001 PHE A 793 TRP 0.007 0.001 TRP B 156 HIS 0.004 0.001 HIS C 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (22768) covalent geometry : angle 0.55501 / 0.28 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04990 / 3.21 ( 1002) hydrogen bonds : angle 4.15818 / 3.02 ( 2988) link_ALPHA1-3 : bond 0.00631 / 0.45 ( 6) link_ALPHA1-3 : angle 2.43111 / 1.25 ( 18) link_ALPHA1-6 : bond 0.00617 / 0.43 ( 4) link_ALPHA1-6 : angle 1.28945 / 0.72 ( 12) link_BETA1-2 : bond 0.00676 / 0.40 ( 2) link_BETA1-2 : angle 3.58578 / 1.72 ( 6) link_BETA1-4 : bond 0.00561 / 0.35 ( 14) link_BETA1-4 : angle 2.58299 / 1.51 ( 42) link_BETA1-6 : bond 0.00139 / 0.11 ( 4) link_BETA1-6 : angle 1.45032 / 0.79 ( 12) link_NAG-ASN : bond 0.00321 / 0.22 ( 8) link_NAG-ASN : angle 2.53874 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8628 (t0) REVERT: D 200 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7383 (tp30) REVERT: C 52 HIS cc_start: 0.4062 (t70) cc_final: 0.3729 (t70) REVERT: C 309 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8989 (tt) REVERT: C 520 THR cc_start: 0.5790 (OUTLIER) cc_final: 0.5282 (p) REVERT: C 535 LYS cc_start: 0.6178 (mttt) cc_final: 0.5438 (ttpp) REVERT: C 671 LYS cc_start: 0.6724 (ptpp) cc_final: 0.6492 (ptpp) REVERT: C 911 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8222 (ptt-90) REVERT: E 13 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 203 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: A 215 ASN cc_start: 0.6338 (m-40) cc_final: 0.5850 (p0) REVERT: A 309 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 534 MET cc_start: 0.4933 (mmp) cc_final: 0.4111 (mmm) REVERT: A 535 LYS cc_start: 0.5749 (mttt) cc_final: 0.5080 (ttpp) outliers start: 46 outliers final: 35 residues processed: 194 average time/residue: 0.1373 time to fit residues: 41.8720 Evaluate side-chains 189 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 81 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 226 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105111 restraints weight = 39564.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099332 restraints weight = 35541.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101611 restraints weight = 38667.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100682 restraints weight = 27454.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101909 restraints weight = 23918.325| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 22806 Z= 0.104 Angle : 0.541 12.766 30850 Z= 0.264 Chirality : 0.040 0.388 3492 Planarity : 0.004 0.052 3774 Dihedral : 11.087 147.409 3528 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.78 % Allowed : 17.63 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.96 (0.17), residues: 2630 helix: 1.80 (0.15), residues: 1186 sheet: 0.33 (0.31), residues: 268 loop : -0.46 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 223 TYR 0.017 0.001 TYR A 869 PHE 0.014 0.001 PHE B 25 TRP 0.008 0.001 TRP A 931 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (22768) covalent geometry : angle 0.52460 / 0.26 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04112 / 2.64 ( 1002) hydrogen bonds : angle 4.02908 / 2.93 ( 2988) link_ALPHA1-3 : bond 0.00673 / 0.48 ( 6) link_ALPHA1-3 : angle 2.44362 / 1.25 ( 18) link_ALPHA1-6 : bond 0.00638 / 0.44 ( 4) link_ALPHA1-6 : angle 1.30848 / 0.72 ( 12) link_BETA1-2 : bond 0.00630 / 0.37 ( 2) link_BETA1-2 : angle 3.65162 / 1.75 ( 6) link_BETA1-4 : bond 0.00616 / 0.39 ( 14) link_BETA1-4 : angle 2.36257 / 1.40 ( 42) link_BETA1-6 : bond 0.00069 / 0.05 ( 4) link_BETA1-6 : angle 1.34962 / 0.75 ( 12) link_NAG-ASN : bond 0.00522 / 0.37 ( 8) link_NAG-ASN : angle 2.04218 / 1.69 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8543 (t0) REVERT: D 200 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7420 (tp30) REVERT: C 52 HIS cc_start: 0.3950 (t70) cc_final: 0.3611 (t70) REVERT: C 309 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9045 (tt) REVERT: C 520 THR cc_start: 0.5622 (OUTLIER) cc_final: 0.5261 (p) REVERT: C 671 LYS cc_start: 0.6595 (ptpp) cc_final: 0.6364 (ptpp) REVERT: E 13 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 203 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: A 215 ASN cc_start: 0.6197 (m-40) cc_final: 0.5832 (p0) REVERT: A 309 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8892 (tt) REVERT: A 483 ASN cc_start: 0.5540 (m-40) cc_final: 0.5035 (t0) REVERT: A 534 MET cc_start: 0.4941 (mmp) cc_final: 0.4098 (mmm) REVERT: A 535 LYS cc_start: 0.5633 (mttt) cc_final: 0.5011 (ttpp) outliers start: 40 outliers final: 32 residues processed: 191 average time/residue: 0.1439 time to fit residues: 43.4155 Evaluate side-chains 187 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.139692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102447 restraints weight = 39010.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098016 restraints weight = 45844.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099446 restraints weight = 41884.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101225 restraints weight = 27021.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101410 restraints weight = 24262.823| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22806 Z= 0.173 Angle : 0.597 12.130 30850 Z= 0.292 Chirality : 0.042 0.379 3492 Planarity : 0.004 0.051 3774 Dihedral : 11.330 146.791 3524 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.09 % Allowed : 17.41 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2630 helix: 1.65 (0.15), residues: 1186 sheet: 0.28 (0.31), residues: 260 loop : -0.47 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 67 TYR 0.018 0.001 TYR D 248 PHE 0.020 0.002 PHE A 793 TRP 0.008 0.001 TRP C 105 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (22768) covalent geometry : angle 0.58198 / 0.29 (30730) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05164 / 3.33 ( 1002) hydrogen bonds : angle 4.14999 / 3.02 ( 2988) link_ALPHA1-3 : bond 0.00582 / 0.41 ( 6) link_ALPHA1-3 : angle 2.40886 / 1.24 ( 18) link_ALPHA1-6 : bond 0.00635 / 0.44 ( 4) link_ALPHA1-6 : angle 1.27497 / 0.71 ( 12) link_BETA1-2 : bond 0.00682 / 0.40 ( 2) link_BETA1-2 : angle 3.55421 / 1.71 ( 6) link_BETA1-4 : bond 0.00511 / 0.32 ( 14) link_BETA1-4 : angle 2.46855 / 1.47 ( 42) link_BETA1-6 : bond 0.00150 / 0.11 ( 4) link_BETA1-6 : angle 1.43197 / 0.78 ( 12) link_NAG-ASN : bond 0.00426 / 0.32 ( 8) link_NAG-ASN : angle 2.14741 / 1.81 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.25 seconds wall clock time: 57 minutes 5.22 seconds (3425.22 seconds total)