Starting phenix.real_space_refine on Thu Jun 19 20:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfz_36220/06_2025/8jfz_36220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfz_36220/06_2025/8jfz_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_36220/06_2025/8jfz_36220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfz_36220/06_2025/8jfz_36220.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfz_36220/06_2025/8jfz_36220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfz_36220/06_2025/8jfz_36220.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 14.82, per 1000 atoms: 0.66 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: 6.54 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.68 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: 8.65 Time building geometry restraints manager: 7.53 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: 13804 30.66 - 61.31: 802 61.31 - 91.97: 84 91.97 - 122.62: 46 122.62 - 153.28: 8 Dihedral angle restraints: 14744 sinusoidal: 7124 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 14741 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 1023 or resid 1101 or resid 1104 through 1110)) \ selection = (chain 'C' and (resid 37 through 1023 or resid 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 or 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 O4 \ P 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.990 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 18.974 153.281 9844 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP D 156 HIS 0.010 0.003 HIS A 557 PHE 0.036 0.004 PHE C 100 TYR 0.028 0.003 TYR A 970 ARG 0.017 0.002 ARG C 893 Details of bonding type rmsd link_NAG-ASN : bond 0.01413 ( 8) link_NAG-ASN : angle 3.40218 ( 24) link_ALPHA1-6 : bond 0.00743 ( 4) link_ALPHA1-6 : angle 1.28238 ( 12) link_BETA1-2 : bond 0.00979 ( 2) link_BETA1-2 : angle 5.34523 ( 6) link_BETA1-4 : bond 0.00862 ( 14) link_BETA1-4 : angle 5.98596 ( 42) link_ALPHA1-3 : bond 0.00816 ( 6) link_ALPHA1-3 : angle 3.04808 ( 18) hydrogen bonds : bond 0.15870 ( 1002) hydrogen bonds : angle 7.08693 ( 2988) link_BETA1-6 : bond 0.00273 ( 4) link_BETA1-6 : angle 1.04426 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.01118 (22768) covalent geometry : angle 1.55408 (30730) *********************** 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 : 2.597 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: 0.7616 (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: 0.8642 (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: 0.7980 (mm-40) REVERT: B 156 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (m-10) REVERT: B 207 ASN cc_start: 0.8447 (t0) cc_final: 0.8195 (t0) 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: 0.7671 (mm) REVERT: A 224 PRO cc_start: 0.6319 (Cg_exo) cc_final: 0.5995 (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: 0.6951 (tp) REVERT: A 734 MET cc_start: 0.8825 (mmp) cc_final: 0.8596 (mmm) REVERT: A 794 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 849 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 1023 TYR cc_start: 0.8608 (p90) cc_final: 0.8268 (p90) outliers start: 169 outliers final: 22 residues processed: 573 average time/residue: 0.4214 time to fit residues: 350.4171 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 : 2.309 ------------------------------------------------------------------------------- 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 221 optimal weight: 0.6980 chunk 198 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 56 GLN 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 474 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 A 942 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112812 restraints weight = 39159.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109102 restraints weight = 35971.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110305 restraints weight = 34137.780| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22806 Z= 0.168 Angle : 0.718 10.961 30850 Z= 0.353 Chirality : 0.047 0.438 3492 Planarity : 0.007 0.076 3774 Dihedral : 16.556 147.685 4973 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.37 % Allowed : 13.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2630 helix: 1.30 (0.15), residues: 1152 sheet: -1.16 (0.28), residues: 274 loop : -1.26 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 156 HIS 0.011 0.001 HIS A 398 PHE 0.020 0.002 PHE C 793 TYR 0.015 0.001 TYR C 55 ARG 0.008 0.001 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 8) link_NAG-ASN : angle 2.52362 ( 24) link_ALPHA1-6 : bond 0.00717 ( 4) link_ALPHA1-6 : angle 2.03780 ( 12) link_BETA1-2 : bond 0.00533 ( 2) link_BETA1-2 : angle 5.03317 ( 6) link_BETA1-4 : bond 0.01013 ( 14) link_BETA1-4 : angle 3.77170 ( 42) link_ALPHA1-3 : bond 0.00972 ( 6) link_ALPHA1-3 : angle 3.84358 ( 18) hydrogen bonds : bond 0.06606 ( 1002) hydrogen bonds : angle 4.94765 ( 2988) link_BETA1-6 : bond 0.00222 ( 4) link_BETA1-6 : angle 1.69759 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00374 (22768) covalent geometry : angle 0.69023 (30730) *********************** 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 272 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 395 ASN cc_start: 0.5762 (t0) cc_final: 0.5404 (t0) REVERT: C 470 MET cc_start: 0.6935 (mmm) cc_final: 0.6526 (mmt) REVERT: C 794 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 911 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7554 (ptt180) REVERT: E 13 THR cc_start: 0.8515 (m) cc_final: 0.8184 (p) REVERT: B 159 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 180 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8598 (ttpp) REVERT: A 55 TYR cc_start: 0.4007 (m-80) cc_final: 0.3666 (m-80) REVERT: A 164 MET cc_start: 0.7574 (mtt) cc_final: 0.7366 (ttm) REVERT: A 199 ILE cc_start: 0.8154 (mm) cc_final: 0.7885 (mm) REVERT: A 202 ASP cc_start: 0.5569 (m-30) cc_final: 0.5317 (m-30) REVERT: A 206 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6552 (pt) REVERT: A 534 MET cc_start: 0.5024 (mmp) cc_final: 0.4402 (mmm) REVERT: A 734 MET cc_start: 0.8872 (mmp) cc_final: 0.8638 (mmm) REVERT: A 911 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6965 (ptt180) REVERT: G 10 GLU cc_start: 0.7405 (tp30) cc_final: 0.7137 (tp30) outliers start: 76 outliers final: 38 residues processed: 257 average time/residue: 0.3770 time to fit residues: 150.5844 Evaluate side-chains 199 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 203 GLN Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 123 ASP 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 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 911 ARG Chi-restraints excluded: chain C residue 1002 ASP 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 B residue 287 TYR 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 163 ASN 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 615 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 794 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 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 52 optimal weight: 0.0030 chunk 21 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 620 HIS C 720 ASN B 264 GLN B 271 ASN A 209 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.146928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108419 restraints weight = 38954.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105438 restraints weight = 37497.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106458 restraints weight = 38843.463| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22806 Z= 0.166 Angle : 0.653 10.226 30850 Z= 0.320 Chirality : 0.046 0.410 3492 Planarity : 0.006 0.057 3774 Dihedral : 14.882 149.158 4937 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 13.90 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2630 helix: 1.68 (0.15), residues: 1168 sheet: -0.58 (0.28), residues: 282 loop : -0.85 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 156 HIS 0.009 0.002 HIS A 209 PHE 0.019 0.002 PHE C 793 TYR 0.018 0.001 TYR D 248 ARG 0.006 0.001 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 1.85858 ( 24) link_ALPHA1-6 : bond 0.00743 ( 4) link_ALPHA1-6 : angle 1.75413 ( 12) link_BETA1-2 : bond 0.00572 ( 2) link_BETA1-2 : angle 4.57413 ( 6) link_BETA1-4 : bond 0.00633 ( 14) link_BETA1-4 : angle 3.41219 ( 42) link_ALPHA1-3 : bond 0.01199 ( 6) link_ALPHA1-3 : angle 3.34964 ( 18) hydrogen bonds : bond 0.05520 ( 1002) hydrogen bonds : angle 4.49783 ( 2988) link_BETA1-6 : bond 0.00171 ( 4) link_BETA1-6 : angle 1.56804 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00384 (22768) covalent geometry : angle 0.62974 (30730) *********************** 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 258 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 2.351 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: symmetry clash revert: symmetry clash REVERT: D 200 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7570 (tp30) REVERT: C 170 LEU cc_start: 0.6332 (mt) cc_final: 0.6131 (mt) REVERT: C 346 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 391 MET cc_start: 0.5704 (mpp) cc_final: 0.5395 (mpp) REVERT: C 470 MET cc_start: 0.6775 (mmm) cc_final: 0.6569 (mmt) REVERT: C 553 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7561 (pt) REVERT: C 911 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7821 (ptt90) REVERT: E 10 GLU cc_start: 0.7341 (tp30) cc_final: 0.7108 (tp30) REVERT: E 13 THR cc_start: 0.8527 (m) cc_final: 0.8316 (p) REVERT: B 180 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8551 (ttpp) REVERT: A 199 ILE cc_start: 0.8326 (mm) cc_final: 0.8082 (mm) REVERT: A 202 ASP cc_start: 0.5565 (m-30) cc_final: 0.5304 (m-30) REVERT: A 395 ASN cc_start: 0.4941 (t0) cc_final: 0.4665 (t0) REVERT: A 489 GLN cc_start: 0.3575 (tp40) cc_final: 0.3352 (tp40) REVERT: A 534 MET cc_start: 0.4962 (mmp) cc_final: 0.4347 (mmm) REVERT: A 543 LEU cc_start: 0.8135 (tp) cc_final: 0.7917 (mm) REVERT: A 699 LEU cc_start: 0.8135 (tp) cc_final: 0.7228 (tp) REVERT: A 780 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8853 (mp) REVERT: A 847 GLU cc_start: 0.7681 (pp20) cc_final: 0.7442 (pp20) REVERT: G 14 TYR cc_start: 0.8646 (t80) cc_final: 0.8412 (t80) outliers start: 79 outliers final: 42 residues processed: 244 average time/residue: 0.3756 time to fit residues: 141.2337 Evaluate side-chains 197 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 154 SER 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 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 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 73 VAL 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 B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR 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 550 GLU Chi-restraints excluded: chain A residue 623 THR 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 G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 249 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.147201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109497 restraints weight = 38894.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106646 restraints weight = 42801.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107852 restraints weight = 38948.937| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22806 Z= 0.124 Angle : 0.580 11.531 30850 Z= 0.279 Chirality : 0.043 0.422 3492 Planarity : 0.005 0.050 3774 Dihedral : 13.974 148.590 4929 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.40 % Allowed : 15.10 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2630 helix: 1.88 (0.15), residues: 1170 sheet: -0.37 (0.29), residues: 268 loop : -0.76 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 156 HIS 0.008 0.001 HIS A 209 PHE 0.018 0.001 PHE B 25 TYR 0.013 0.001 TYR A 869 ARG 0.006 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 1.70557 ( 24) link_ALPHA1-6 : bond 0.00707 ( 4) link_ALPHA1-6 : angle 1.93941 ( 12) link_BETA1-2 : bond 0.00403 ( 2) link_BETA1-2 : angle 4.45579 ( 6) link_BETA1-4 : bond 0.00624 ( 14) link_BETA1-4 : angle 3.19539 ( 42) link_ALPHA1-3 : bond 0.01121 ( 6) link_ALPHA1-3 : angle 3.61039 ( 18) hydrogen bonds : bond 0.04876 ( 1002) hydrogen bonds : angle 4.33218 ( 2988) link_BETA1-6 : bond 0.00091 ( 4) link_BETA1-6 : angle 1.59139 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00274 (22768) covalent geometry : angle 0.55464 (30730) *********************** 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 210 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 2.399 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 160 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (m) REVERT: D 200 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7620 (tp30) REVERT: C 470 MET cc_start: 0.6684 (mmm) cc_final: 0.6454 (mmt) REVERT: C 832 MET cc_start: 0.8355 (mmt) cc_final: 0.7987 (mmt) REVERT: C 911 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7808 (ptt180) REVERT: E 10 GLU cc_start: 0.7337 (tp30) cc_final: 0.7110 (tp30) REVERT: B 95 ASN cc_start: 0.8098 (t0) cc_final: 0.7870 (m-40) REVERT: B 180 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: B 223 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7346 (ttm-80) REVERT: A 199 ILE cc_start: 0.8466 (mm) cc_final: 0.8241 (mm) REVERT: A 267 MET cc_start: 0.7394 (tpp) cc_final: 0.7114 (tpp) REVERT: A 395 ASN cc_start: 0.5107 (t0) cc_final: 0.4896 (t0) REVERT: A 534 MET cc_start: 0.4769 (mmp) cc_final: 0.4170 (mmm) REVERT: A 911 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7887 (ptt-90) outliers start: 54 outliers final: 32 residues processed: 197 average time/residue: 0.3483 time to fit residues: 107.4925 Evaluate side-chains 180 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 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 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 295 ILE 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 550 GLU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 894 TRP 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 90 SER 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 B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU 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 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 677 VAL 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 254 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.144758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106923 restraints weight = 39014.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102941 restraints weight = 43261.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104731 restraints weight = 37080.707| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22806 Z= 0.167 Angle : 0.608 13.075 30850 Z= 0.291 Chirality : 0.045 0.442 3492 Planarity : 0.005 0.101 3774 Dihedral : 13.559 150.848 4929 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.33 % Allowed : 14.56 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2630 helix: 1.78 (0.15), residues: 1170 sheet: -0.10 (0.28), residues: 304 loop : -0.65 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.011 0.001 HIS A 209 PHE 0.019 0.001 PHE C 793 TYR 0.018 0.001 TYR D 248 ARG 0.015 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 8) link_NAG-ASN : angle 1.73871 ( 24) link_ALPHA1-6 : bond 0.00697 ( 4) link_ALPHA1-6 : angle 1.86481 ( 12) link_BETA1-2 : bond 0.00445 ( 2) link_BETA1-2 : angle 4.32043 ( 6) link_BETA1-4 : bond 0.00564 ( 14) link_BETA1-4 : angle 3.16936 ( 42) link_ALPHA1-3 : bond 0.01027 ( 6) link_ALPHA1-3 : angle 3.57787 ( 18) hydrogen bonds : bond 0.05227 ( 1002) hydrogen bonds : angle 4.32511 ( 2988) link_BETA1-6 : bond 0.00100 ( 4) link_BETA1-6 : angle 1.59986 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00396 (22768) covalent geometry : angle 0.58433 (30730) *********************** 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 238 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 2.378 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: symmetry clash REVERT: D 159 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8485 (t0) REVERT: D 160 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7843 (m) REVERT: D 200 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7749 (tp30) REVERT: C 346 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8733 (tp) REVERT: C 520 THR cc_start: 0.5708 (OUTLIER) cc_final: 0.5216 (p) REVERT: C 700 ILE cc_start: 0.8406 (mt) cc_final: 0.8183 (mm) REVERT: C 780 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8691 (mp) REVERT: C 832 MET cc_start: 0.8387 (mmt) cc_final: 0.8040 (mmt) REVERT: C 911 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8119 (ptt180) REVERT: B 223 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7431 (ttm-80) REVERT: A 70 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6748 (tm-30) REVERT: A 90 ILE cc_start: 0.6361 (OUTLIER) cc_final: 0.6097 (mt) REVERT: A 164 MET cc_start: 0.8641 (ttm) cc_final: 0.8222 (tpp) REVERT: A 267 MET cc_start: 0.7425 (tpp) cc_final: 0.7057 (tpp) REVERT: A 395 ASN cc_start: 0.5208 (t0) cc_final: 0.4927 (t0) REVERT: A 534 MET cc_start: 0.4907 (mmp) cc_final: 0.4255 (mmm) REVERT: A 780 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8741 (mp) REVERT: A 911 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8079 (ptt180) outliers start: 75 outliers final: 49 residues processed: 227 average time/residue: 0.3749 time to fit residues: 135.8760 Evaluate side-chains 206 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR 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 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 155 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 311 LEU Chi-restraints excluded: chain C residue 346 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 550 GLU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 841 THR 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 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 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR 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 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 364 VAL 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 460 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 136 optimal weight: 0.5980 overall best weight: 5.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 474 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103092 restraints weight = 39078.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098306 restraints weight = 41758.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099511 restraints weight = 42675.986| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 22806 Z= 0.319 Angle : 0.780 14.411 30850 Z= 0.383 Chirality : 0.051 0.432 3492 Planarity : 0.006 0.078 3774 Dihedral : 14.141 160.566 4928 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.53 % Allowed : 14.08 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2630 helix: 1.17 (0.15), residues: 1164 sheet: -0.31 (0.29), residues: 304 loop : -0.79 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 105 HIS 0.065 0.003 HIS A 209 PHE 0.038 0.002 PHE C 793 TYR 0.038 0.002 TYR D 248 ARG 0.016 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 1.98327 ( 24) link_ALPHA1-6 : bond 0.00618 ( 4) link_ALPHA1-6 : angle 1.94747 ( 12) link_BETA1-2 : bond 0.00732 ( 2) link_BETA1-2 : angle 4.03929 ( 6) link_BETA1-4 : bond 0.00511 ( 14) link_BETA1-4 : angle 3.21746 ( 42) link_ALPHA1-3 : bond 0.01008 ( 6) link_ALPHA1-3 : angle 3.46733 ( 18) hydrogen bonds : bond 0.07169 ( 1002) hydrogen bonds : angle 4.72661 ( 2988) link_BETA1-6 : bond 0.00305 ( 4) link_BETA1-6 : angle 1.90709 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00780 (22768) covalent geometry : angle 0.76219 (30730) *********************** 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 265 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 163 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8699 (t0) REVERT: D 160 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (m) REVERT: D 200 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7837 (tp30) REVERT: D 270 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: C 309 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8944 (tt) REVERT: C 346 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8761 (tp) REVERT: C 520 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.5021 (p) REVERT: C 535 LYS cc_start: 0.6300 (mttt) cc_final: 0.5588 (ttpp) REVERT: C 615 MET cc_start: 0.8138 (tpp) cc_final: 0.7933 (tpp) REVERT: C 780 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8801 (mp) REVERT: C 911 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8272 (ptt-90) REVERT: B 159 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8592 (t0) REVERT: B 160 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 90 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6491 (mt) REVERT: A 164 MET cc_start: 0.8667 (ttm) cc_final: 0.8309 (tpp) REVERT: A 309 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 395 ASN cc_start: 0.5493 (t0) cc_final: 0.5272 (t0) REVERT: A 535 LYS cc_start: 0.5692 (mttt) cc_final: 0.5034 (ttpp) REVERT: A 780 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 911 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8303 (ptt180) outliers start: 102 outliers final: 62 residues processed: 253 average time/residue: 0.3261 time to fit residues: 132.3644 Evaluate side-chains 222 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 146 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 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 216 SER Chi-restraints excluded: chain C residue 288 ILE 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 346 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 507 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 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 B residue 29 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 ASN 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 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 193 VAL 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 321 VAL 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 627 ILE Chi-restraints excluded: chain A residue 640 THR 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 921 SER Chi-restraints excluded: chain A residue 974 THR 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 114 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 167 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1019 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.142608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106495 restraints weight = 38734.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101961 restraints weight = 39466.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103157 restraints weight = 39300.857| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22806 Z= 0.138 Angle : 0.597 11.066 30850 Z= 0.289 Chirality : 0.044 0.434 3492 Planarity : 0.004 0.063 3774 Dihedral : 13.400 161.513 4928 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.31 % Allowed : 16.65 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2630 helix: 1.59 (0.15), residues: 1166 sheet: -0.22 (0.29), residues: 302 loop : -0.64 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.010 0.001 HIS A 493 PHE 0.020 0.001 PHE D 25 TYR 0.020 0.001 TYR C 869 ARG 0.012 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 8) link_NAG-ASN : angle 1.59888 ( 24) link_ALPHA1-6 : bond 0.00636 ( 4) link_ALPHA1-6 : angle 1.79188 ( 12) link_BETA1-2 : bond 0.00593 ( 2) link_BETA1-2 : angle 4.20476 ( 6) link_BETA1-4 : bond 0.00552 ( 14) link_BETA1-4 : angle 2.88787 ( 42) link_ALPHA1-3 : bond 0.01042 ( 6) link_ALPHA1-3 : angle 3.68428 ( 18) hydrogen bonds : bond 0.05375 ( 1002) hydrogen bonds : angle 4.35858 ( 2988) link_BETA1-6 : bond 0.00213 ( 4) link_BETA1-6 : angle 1.78047 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00313 (22768) covalent geometry : angle 0.57443 (30730) *********************** 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 208 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8678 (t0) REVERT: D 200 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7727 (tp30) REVERT: D 270 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: C 478 VAL cc_start: 0.2977 (OUTLIER) cc_final: 0.2762 (t) REVERT: C 535 LYS cc_start: 0.6269 (mttt) cc_final: 0.5554 (ttpp) REVERT: C 615 MET cc_start: 0.8044 (tpp) cc_final: 0.7797 (tpp) REVERT: C 780 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 160 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7986 (m) REVERT: A 90 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6356 (mt) REVERT: A 215 ASN cc_start: 0.6332 (m-40) cc_final: 0.5952 (p0) REVERT: A 244 PHE cc_start: 0.6423 (m-80) cc_final: 0.6145 (m-80) REVERT: A 507 MET cc_start: 0.4019 (mmm) cc_final: 0.3585 (mmm) REVERT: A 534 MET cc_start: 0.3592 (tpp) cc_final: 0.3262 (mmm) REVERT: A 535 LYS cc_start: 0.5515 (mttt) cc_final: 0.4884 (ttpp) REVERT: A 911 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7859 (ptt-90) outliers start: 52 outliers final: 34 residues processed: 198 average time/residue: 0.3465 time to fit residues: 108.7977 Evaluate side-chains 190 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 2.589 ------------------------------------------------------------------------------- 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 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 295 ILE 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 478 VAL Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 677 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 895 ILE 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 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 90 ILE 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 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG 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 221 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.142877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105649 restraints weight = 38595.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100906 restraints weight = 35427.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102591 restraints weight = 36921.459| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22806 Z= 0.138 Angle : 0.578 9.301 30850 Z= 0.280 Chirality : 0.043 0.443 3492 Planarity : 0.004 0.061 3774 Dihedral : 12.799 164.037 4923 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 16.65 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2630 helix: 1.67 (0.15), residues: 1168 sheet: -0.16 (0.29), residues: 304 loop : -0.56 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.019 0.001 HIS A 209 PHE 0.020 0.001 PHE D 25 TYR 0.020 0.001 TYR A 869 ARG 0.010 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 8) link_NAG-ASN : angle 1.42061 ( 24) link_ALPHA1-6 : bond 0.00637 ( 4) link_ALPHA1-6 : angle 1.74725 ( 12) link_BETA1-2 : bond 0.00731 ( 2) link_BETA1-2 : angle 4.11436 ( 6) link_BETA1-4 : bond 0.00597 ( 14) link_BETA1-4 : angle 2.77054 ( 42) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 3.69688 ( 18) hydrogen bonds : bond 0.05014 ( 1002) hydrogen bonds : angle 4.23871 ( 2988) link_BETA1-6 : bond 0.00184 ( 4) link_BETA1-6 : angle 1.73579 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00322 (22768) covalent geometry : angle 0.55636 (30730) *********************** 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 219 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (t0) REVERT: D 200 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7686 (tp30) REVERT: C 478 VAL cc_start: 0.2991 (OUTLIER) cc_final: 0.2773 (t) REVERT: C 520 THR cc_start: 0.5396 (OUTLIER) cc_final: 0.4889 (p) REVERT: C 535 LYS cc_start: 0.6315 (mttt) cc_final: 0.5577 (ttpp) REVERT: C 699 LEU cc_start: 0.8229 (tp) cc_final: 0.8027 (tp) REVERT: C 734 MET cc_start: 0.8508 (mmt) cc_final: 0.8304 (mpp) REVERT: C 780 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 159 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (t0) REVERT: B 203 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: A 90 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6303 (mt) REVERT: A 215 ASN cc_start: 0.6366 (m-40) cc_final: 0.5919 (p0) REVERT: A 386 MET cc_start: 0.7411 (mmt) cc_final: 0.7085 (mmt) REVERT: A 507 MET cc_start: 0.4016 (mmm) cc_final: 0.3774 (mmm) REVERT: A 534 MET cc_start: 0.3622 (tpp) cc_final: 0.3256 (mmm) REVERT: A 535 LYS cc_start: 0.5754 (mttt) cc_final: 0.5061 (ttpp) REVERT: A 837 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8073 (ptm160) outliers start: 57 outliers final: 37 residues processed: 209 average time/residue: 0.3431 time to fit residues: 113.2985 Evaluate side-chains 194 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 154 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 288 ILE 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 520 THR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 90 ILE 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 358 VAL 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 826 GLN Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 868 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 176 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.142142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104101 restraints weight = 38955.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100217 restraints weight = 40132.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101468 restraints weight = 37432.748| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 22806 Z= 0.109 Angle : 0.547 9.728 30850 Z= 0.264 Chirality : 0.042 0.440 3492 Planarity : 0.004 0.052 3774 Dihedral : 12.246 164.100 4922 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.73 % Allowed : 17.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2630 helix: 1.80 (0.15), residues: 1170 sheet: -0.01 (0.30), residues: 302 loop : -0.47 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.015 0.001 HIS A 209 PHE 0.018 0.001 PHE C 967 TYR 0.026 0.001 TYR C 488 ARG 0.009 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 8) link_NAG-ASN : angle 1.31587 ( 24) link_ALPHA1-6 : bond 0.00631 ( 4) link_ALPHA1-6 : angle 1.64856 ( 12) link_BETA1-2 : bond 0.00731 ( 2) link_BETA1-2 : angle 4.11508 ( 6) link_BETA1-4 : bond 0.00626 ( 14) link_BETA1-4 : angle 2.63614 ( 42) link_ALPHA1-3 : bond 0.01018 ( 6) link_ALPHA1-3 : angle 3.80665 ( 18) hydrogen bonds : bond 0.04376 ( 1002) hydrogen bonds : angle 4.12766 ( 2988) link_BETA1-6 : bond 0.00120 ( 4) link_BETA1-6 : angle 1.62004 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00239 (22768) covalent geometry : angle 0.52532 (30730) *********************** 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 193 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8620 (t0) REVERT: D 200 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7676 (tp30) REVERT: C 309 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9066 (tt) REVERT: C 520 THR cc_start: 0.5496 (OUTLIER) cc_final: 0.5075 (p) REVERT: C 535 LYS cc_start: 0.6255 (mttt) cc_final: 0.5509 (ttpp) REVERT: C 699 LEU cc_start: 0.8331 (tp) cc_final: 0.8120 (tp) REVERT: C 832 MET cc_start: 0.8040 (mmt) cc_final: 0.7717 (mmt) REVERT: B 159 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8406 (t0) REVERT: B 203 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: A 70 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 215 ASN cc_start: 0.6291 (m-40) cc_final: 0.6039 (p0) REVERT: A 267 MET cc_start: 0.7726 (tpp) cc_final: 0.6938 (tpp) REVERT: A 386 MET cc_start: 0.7155 (mmt) cc_final: 0.6771 (mmt) REVERT: A 507 MET cc_start: 0.4119 (mmm) cc_final: 0.3809 (mmm) REVERT: A 517 ARG cc_start: 0.3575 (mtt180) cc_final: 0.2724 (ttp-170) REVERT: A 534 MET cc_start: 0.3840 (tpp) cc_final: 0.3462 (mmm) REVERT: A 535 LYS cc_start: 0.5763 (mttt) cc_final: 0.5090 (ttpp) REVERT: A 852 MET cc_start: 0.7632 (tpp) cc_final: 0.7378 (tpp) outliers start: 39 outliers final: 26 residues processed: 186 average time/residue: 0.3625 time to fit residues: 105.1694 Evaluate side-chains 178 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 2.379 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU 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 588 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 PHE 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 358 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 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 254 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 235 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.141496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104292 restraints weight = 39251.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100273 restraints weight = 42303.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101572 restraints weight = 39697.374| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22806 Z= 0.119 Angle : 0.554 10.041 30850 Z= 0.268 Chirality : 0.042 0.432 3492 Planarity : 0.004 0.051 3774 Dihedral : 11.995 164.933 4922 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 17.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2630 helix: 1.84 (0.15), residues: 1172 sheet: 0.08 (0.30), residues: 302 loop : -0.41 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.022 0.001 HIS A 209 PHE 0.020 0.001 PHE D 25 TYR 0.019 0.001 TYR A 869 ARG 0.009 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 8) link_NAG-ASN : angle 1.28768 ( 24) link_ALPHA1-6 : bond 0.00588 ( 4) link_ALPHA1-6 : angle 1.62311 ( 12) link_BETA1-2 : bond 0.00841 ( 2) link_BETA1-2 : angle 4.02576 ( 6) link_BETA1-4 : bond 0.00612 ( 14) link_BETA1-4 : angle 2.61084 ( 42) link_ALPHA1-3 : bond 0.01027 ( 6) link_ALPHA1-3 : angle 3.87056 ( 18) hydrogen bonds : bond 0.04479 ( 1002) hydrogen bonds : angle 4.10134 ( 2988) link_BETA1-6 : bond 0.00142 ( 4) link_BETA1-6 : angle 1.60614 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00270 (22768) covalent geometry : angle 0.53196 (30730) ********************** 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 191 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8596 (t0) REVERT: D 200 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7650 (tm-30) REVERT: C 309 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9067 (tt) REVERT: C 520 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5110 (p) REVERT: C 535 LYS cc_start: 0.6426 (mttt) cc_final: 0.5586 (ttpp) REVERT: C 832 MET cc_start: 0.7985 (mmt) cc_final: 0.7721 (mmt) REVERT: B 203 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: A 70 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 215 ASN cc_start: 0.6320 (m-40) cc_final: 0.6057 (p0) REVERT: A 267 MET cc_start: 0.7745 (tpp) cc_final: 0.6969 (tpp) REVERT: A 386 MET cc_start: 0.7208 (mmt) cc_final: 0.6903 (mmt) REVERT: A 534 MET cc_start: 0.3625 (tpp) cc_final: 0.3260 (mmm) REVERT: A 535 LYS cc_start: 0.5735 (mttt) cc_final: 0.5071 (ttpp) outliers start: 41 outliers final: 30 residues processed: 183 average time/residue: 0.3540 time to fit residues: 101.6037 Evaluate side-chains 177 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU 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 588 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 868 SER 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 63 LEU 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 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 358 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 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 203 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 205 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.140421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102399 restraints weight = 38912.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098645 restraints weight = 43872.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099893 restraints weight = 39806.591| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22806 Z= 0.150 Angle : 0.598 16.689 30850 Z= 0.286 Chirality : 0.043 0.423 3492 Planarity : 0.005 0.069 3774 Dihedral : 12.244 165.865 4922 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.82 % Allowed : 17.54 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2630 helix: 1.79 (0.15), residues: 1172 sheet: 0.16 (0.30), residues: 298 loop : -0.41 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.041 0.002 HIS A 209 PHE 0.019 0.001 PHE C 967 TYR 0.018 0.001 TYR A 869 ARG 0.009 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 3.16090 ( 24) link_ALPHA1-6 : bond 0.00538 ( 4) link_ALPHA1-6 : angle 1.60552 ( 12) link_BETA1-2 : bond 0.00903 ( 2) link_BETA1-2 : angle 4.01304 ( 6) link_BETA1-4 : bond 0.00612 ( 14) link_BETA1-4 : angle 2.71589 ( 42) link_ALPHA1-3 : bond 0.01012 ( 6) link_ALPHA1-3 : angle 3.95267 ( 18) hydrogen bonds : bond 0.04824 ( 1002) hydrogen bonds : angle 4.13367 ( 2988) link_BETA1-6 : bond 0.00154 ( 4) link_BETA1-6 : angle 1.61172 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00358 (22768) covalent geometry : angle 0.57158 (30730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7091.64 seconds wall clock time: 125 minutes 20.97 seconds (7520.97 seconds total)