Starting phenix.real_space_refine on Thu May 22 12:55:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfz_36220/05_2025/8jfz_36220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfz_36220/05_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_36220/05_2025/8jfz_36220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfz_36220/05_2025/8jfz_36220.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfz_36220/05_2025/8jfz_36220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfz_36220/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.70, 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: 6.55 Conformation dependent library (CDL) restraints added in 2.7 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: 2.64 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: 8.21 Time building geometry restraints manager: 7.44 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: 1.050 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: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.970 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.990 ------------------------------------------------------------------------------- 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 : 2.452 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: 0.4375 time to fit residues: 362.6472 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 : 2.253 ------------------------------------------------------------------------------- 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 = 0.151058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113303 restraints weight = 39158.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108858 restraints weight = 33985.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110103 restraints weight = 33577.095| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 2.03779 ( 12) link_BETA1-2 : bond 0.00533 ( 2) link_BETA1-2 : angle 5.03316 ( 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 : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 HIS cc_start: 0.3366 (t70) cc_final: 0.3164 (t70) REVERT: C 395 ASN cc_start: 0.5762 (t0) cc_final: 0.5402 (t0) REVERT: C 470 MET cc_start: 0.6936 (mmm) cc_final: 0.6534 (mmt) REVERT: C 794 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8558 (mp) REVERT: C 911 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7574 (ptt180) REVERT: E 13 THR cc_start: 0.8543 (m) cc_final: 0.8226 (p) REVERT: B 159 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 180 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8617 (ttpp) REVERT: A 55 TYR cc_start: 0.4020 (m-80) cc_final: 0.3675 (m-80) REVERT: A 164 MET cc_start: 0.7579 (mtt) cc_final: 0.7365 (ttm) REVERT: A 199 ILE cc_start: 0.8152 (mm) cc_final: 0.7885 (mm) REVERT: A 202 ASP cc_start: 0.5567 (m-30) cc_final: 0.5308 (m-30) REVERT: A 206 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6543 (pt) REVERT: A 534 MET cc_start: 0.5032 (mmp) cc_final: 0.4405 (mmm) REVERT: A 734 MET cc_start: 0.8855 (mmp) cc_final: 0.8623 (mmm) REVERT: A 911 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6977 (ptt180) REVERT: G 10 GLU cc_start: 0.7385 (tp30) cc_final: 0.7128 (tp30) outliers start: 76 outliers final: 38 residues processed: 257 average time/residue: 0.3633 time to fit residues: 144.1970 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 : 2.390 ------------------------------------------------------------------------------- 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: 0.0000 chunk 21 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 230 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.148066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110197 restraints weight = 39018.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105418 restraints weight = 34496.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107456 restraints weight = 34175.394| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22806 Z= 0.162 Angle : 0.637 10.178 30850 Z= 0.312 Chirality : 0.045 0.413 3492 Planarity : 0.006 0.056 3774 Dihedral : 14.862 148.189 4937 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.33 % Allowed : 13.99 % Favored : 82.68 % 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: 0.50 (0.16), residues: 2630 helix: 1.74 (0.15), residues: 1168 sheet: -0.59 (0.28), residues: 284 loop : -0.88 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 156 HIS 0.009 0.001 HIS A 209 PHE 0.028 0.002 PHE D 25 TYR 0.017 0.001 TYR D 206 ARG 0.006 0.001 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 8) link_NAG-ASN : angle 1.84697 ( 24) link_ALPHA1-6 : bond 0.00606 ( 4) link_ALPHA1-6 : angle 1.75910 ( 12) link_BETA1-2 : bond 0.00438 ( 2) link_BETA1-2 : angle 4.68911 ( 6) link_BETA1-4 : bond 0.00535 ( 14) link_BETA1-4 : angle 3.41693 ( 42) link_ALPHA1-3 : bond 0.01107 ( 6) link_ALPHA1-3 : angle 3.40444 ( 18) hydrogen bonds : bond 0.05363 ( 1002) hydrogen bonds : angle 4.47273 ( 2988) link_BETA1-6 : bond 0.00216 ( 4) link_BETA1-6 : angle 1.55689 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00350 (22768) covalent geometry : angle 0.61271 (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 254 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 179 time to evaluate : 2.243 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: 0.7953 (mm-30) cc_final: 0.7562 (tp30) REVERT: C 170 LEU cc_start: 0.6196 (mt) cc_final: 0.5971 (mt) REVERT: C 346 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8767 (tp) REVERT: C 391 MET cc_start: 0.5654 (mpp) cc_final: 0.5312 (mpp) REVERT: C 395 ASN cc_start: 0.5473 (t0) cc_final: 0.5272 (t0) REVERT: C 553 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7538 (pt) REVERT: C 911 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7843 (ptt90) REVERT: E 10 GLU cc_start: 0.7328 (tp30) cc_final: 0.7094 (tp30) REVERT: E 13 THR cc_start: 0.8498 (m) cc_final: 0.8293 (p) REVERT: A 199 ILE cc_start: 0.8235 (mm) cc_final: 0.7974 (mm) REVERT: A 202 ASP cc_start: 0.5577 (m-30) cc_final: 0.5269 (m-30) REVERT: A 395 ASN cc_start: 0.4879 (t0) cc_final: 0.4572 (t0) REVERT: A 489 GLN cc_start: 0.3503 (tp40) cc_final: 0.3257 (tp40) REVERT: A 534 MET cc_start: 0.4986 (mmp) cc_final: 0.4359 (mmm) REVERT: A 699 LEU cc_start: 0.8115 (tp) cc_final: 0.7244 (tp) REVERT: A 780 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 847 GLU cc_start: 0.7669 (pp20) cc_final: 0.7435 (pp20) outliers start: 75 outliers final: 38 residues processed: 240 average time/residue: 0.3548 time to fit residues: 129.7864 Evaluate side-chains 192 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 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 841 THR 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 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 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 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 881 MET 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: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.145993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108486 restraints weight = 38896.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104475 restraints weight = 44046.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106112 restraints weight = 38460.947| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22806 Z= 0.150 Angle : 0.603 12.324 30850 Z= 0.291 Chirality : 0.045 0.421 3492 Planarity : 0.005 0.051 3774 Dihedral : 13.944 149.279 4929 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.40 % Allowed : 14.74 % Favored : 82.86 % 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: 0.66 (0.16), residues: 2630 helix: 1.81 (0.15), residues: 1170 sheet: -0.43 (0.28), residues: 280 loop : -0.73 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 890 HIS 0.017 0.001 HIS A 209 PHE 0.019 0.001 PHE B 25 TYR 0.016 0.001 TYR D 248 ARG 0.005 0.001 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 8) link_NAG-ASN : angle 1.68886 ( 24) link_ALPHA1-6 : bond 0.00686 ( 4) link_ALPHA1-6 : angle 1.94200 ( 12) link_BETA1-2 : bond 0.00411 ( 2) link_BETA1-2 : angle 4.39622 ( 6) link_BETA1-4 : bond 0.00604 ( 14) link_BETA1-4 : angle 3.20269 ( 42) link_ALPHA1-3 : bond 0.01099 ( 6) link_ALPHA1-3 : angle 3.59679 ( 18) hydrogen bonds : bond 0.05211 ( 1002) hydrogen bonds : angle 4.37024 ( 2988) link_BETA1-6 : bond 0.00069 ( 4) link_BETA1-6 : angle 1.60233 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00349 (22768) covalent geometry : angle 0.57866 (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 : 2.271 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: 0.8151 (OUTLIER) cc_final: 0.7860 (m) REVERT: D 200 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7698 (tp30) REVERT: C 832 MET cc_start: 0.8385 (mmt) cc_final: 0.8025 (mmt) REVERT: C 911 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7969 (ptt-90) REVERT: E 10 GLU cc_start: 0.7382 (tp30) cc_final: 0.6980 (tp30) REVERT: E 13 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (p) REVERT: B 223 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7366 (ttm-80) REVERT: A 70 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 164 MET cc_start: 0.8626 (ttm) cc_final: 0.8258 (tpp) REVERT: A 267 MET cc_start: 0.7450 (tpp) cc_final: 0.7162 (tpp) REVERT: A 395 ASN cc_start: 0.5106 (t0) cc_final: 0.4877 (t0) REVERT: A 534 MET cc_start: 0.4828 (mmp) cc_final: 0.4274 (mmm) REVERT: A 911 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8086 (ptt180) outliers start: 54 outliers final: 36 residues processed: 200 average time/residue: 0.3330 time to fit residues: 104.1952 Evaluate side-chains 182 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 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 372 THR Chi-restraints excluded: chain C residue 419 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 712 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 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 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 254 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 chunk 71 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.141545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104538 restraints weight = 39206.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099490 restraints weight = 38642.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101180 restraints weight = 44359.688| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22806 Z= 0.168 Angle : 0.614 13.686 30850 Z= 0.295 Chirality : 0.045 0.443 3492 Planarity : 0.005 0.153 3774 Dihedral : 13.479 152.059 4928 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.60 % Allowed : 14.08 % Favored : 82.33 % 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: 0.77 (0.16), residues: 2630 helix: 1.77 (0.15), residues: 1166 sheet: -0.07 (0.28), residues: 302 loop : -0.60 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 105 HIS 0.006 0.001 HIS C 44 PHE 0.019 0.002 PHE C 793 TYR 0.020 0.001 TYR D 248 ARG 0.020 0.001 ARG C 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 1.62269 ( 24) link_ALPHA1-6 : bond 0.00696 ( 4) link_ALPHA1-6 : angle 1.83686 ( 12) link_BETA1-2 : bond 0.00513 ( 2) link_BETA1-2 : angle 4.26463 ( 6) link_BETA1-4 : bond 0.00572 ( 14) link_BETA1-4 : angle 3.18420 ( 42) link_ALPHA1-3 : bond 0.01107 ( 6) link_ALPHA1-3 : angle 3.60255 ( 18) hydrogen bonds : bond 0.05339 ( 1002) hydrogen bonds : angle 4.37161 ( 2988) link_BETA1-6 : bond 0.00111 ( 4) link_BETA1-6 : angle 1.62922 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00400 (22768) covalent geometry : angle 0.59084 (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 247 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 166 time to evaluate : 2.622 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: 0.8930 (OUTLIER) cc_final: 0.8546 (t0) REVERT: D 160 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7877 (m) REVERT: D 200 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7801 (tp30) REVERT: C 346 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 520 THR cc_start: 0.5760 (OUTLIER) cc_final: 0.5254 (p) REVERT: C 700 ILE cc_start: 0.8432 (mt) cc_final: 0.8207 (mm) REVERT: C 780 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 832 MET cc_start: 0.8384 (mmt) cc_final: 0.8021 (mmt) REVERT: C 911 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8075 (ptt180) REVERT: B 223 ARG cc_start: 0.7697 (tpp80) cc_final: 0.7453 (ttm-80) REVERT: A 70 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 164 MET cc_start: 0.8657 (ttm) cc_final: 0.8309 (tpp) REVERT: A 244 PHE cc_start: 0.7007 (m-80) cc_final: 0.6737 (m-80) REVERT: A 267 MET cc_start: 0.7453 (tpp) cc_final: 0.7127 (tpp) REVERT: A 395 ASN cc_start: 0.5146 (t0) cc_final: 0.4882 (t0) REVERT: A 534 MET cc_start: 0.4871 (mmp) cc_final: 0.4185 (mmm) REVERT: A 543 LEU cc_start: 0.8277 (tp) cc_final: 0.8076 (mm) REVERT: A 780 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 911 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7927 (ptt180) outliers start: 81 outliers final: 49 residues processed: 236 average time/residue: 0.3414 time to fit residues: 126.8625 Evaluate side-chains 204 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 154 SER 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 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 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 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 THR 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 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 1007 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- 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 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 = 0.4037 r_free = 0.4037 target = 0.144535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107851 restraints weight = 38620.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103183 restraints weight = 38829.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104341 restraints weight = 38150.824| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22806 Z= 0.141 Angle : 0.578 14.178 30850 Z= 0.277 Chirality : 0.044 0.450 3492 Planarity : 0.004 0.060 3774 Dihedral : 13.093 153.121 4928 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.06 % Allowed : 14.88 % Favored : 82.06 % 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: 0.85 (0.16), residues: 2630 helix: 1.84 (0.15), residues: 1168 sheet: -0.05 (0.29), residues: 302 loop : -0.56 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 89 HIS 0.017 0.001 HIS A 209 PHE 0.015 0.001 PHE B 25 TYR 0.016 0.001 TYR A 869 ARG 0.005 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 8) link_NAG-ASN : angle 1.58868 ( 24) link_ALPHA1-6 : bond 0.00682 ( 4) link_ALPHA1-6 : angle 1.80313 ( 12) link_BETA1-2 : bond 0.00543 ( 2) link_BETA1-2 : angle 4.25933 ( 6) link_BETA1-4 : bond 0.00552 ( 14) link_BETA1-4 : angle 2.98817 ( 42) link_ALPHA1-3 : bond 0.01087 ( 6) link_ALPHA1-3 : angle 3.65782 ( 18) hydrogen bonds : bond 0.05018 ( 1002) hydrogen bonds : angle 4.24742 ( 2988) link_BETA1-6 : bond 0.00093 ( 4) link_BETA1-6 : angle 1.65660 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00325 (22768) covalent geometry : angle 0.55416 (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 227 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8547 (t0) REVERT: D 160 CYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (m) REVERT: D 200 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7748 (tp30) REVERT: D 270 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: C 155 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7517 (p) REVERT: C 309 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8975 (tt) REVERT: C 346 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8775 (tp) REVERT: C 700 ILE cc_start: 0.8379 (mt) cc_final: 0.8163 (mm) REVERT: C 780 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 832 MET cc_start: 0.8411 (mmt) cc_final: 0.8044 (mmt) REVERT: C 911 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8161 (ptt-90) REVERT: B 159 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8350 (t0) REVERT: B 223 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7435 (ttm-80) REVERT: A 164 MET cc_start: 0.8611 (ttm) cc_final: 0.8276 (tpp) REVERT: A 244 PHE cc_start: 0.6891 (m-80) cc_final: 0.6680 (m-80) REVERT: A 267 MET cc_start: 0.7415 (tpp) cc_final: 0.7009 (tpp) REVERT: A 395 ASN cc_start: 0.5477 (t0) cc_final: 0.5250 (t0) REVERT: A 534 MET cc_start: 0.4842 (mmp) cc_final: 0.4114 (mmm) REVERT: A 780 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 911 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7951 (ptt180) outliers start: 69 outliers final: 44 residues processed: 216 average time/residue: 0.3188 time to fit residues: 109.0260 Evaluate side-chains 201 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 159 ASN Chi-restraints excluded: chain D residue 160 CYS 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 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 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 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG 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 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 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 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 114 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 37 optimal weight: 40.0000 chunk 167 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** C1019 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4009 r_free = 0.4009 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106323 restraints weight = 38709.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101145 restraints weight = 36318.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103076 restraints weight = 40186.448| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22806 Z= 0.189 Angle : 0.622 14.757 30850 Z= 0.301 Chirality : 0.045 0.460 3492 Planarity : 0.005 0.061 3774 Dihedral : 12.891 157.480 4928 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.37 % Allowed : 14.70 % Favored : 81.93 % 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: 0.72 (0.16), residues: 2630 helix: 1.68 (0.15), residues: 1168 sheet: -0.11 (0.29), residues: 302 loop : -0.57 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 105 HIS 0.010 0.001 HIS A 493 PHE 0.023 0.002 PHE C 793 TYR 0.022 0.002 TYR D 248 ARG 0.012 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 8) link_NAG-ASN : angle 1.63032 ( 24) link_ALPHA1-6 : bond 0.00642 ( 4) link_ALPHA1-6 : angle 1.75579 ( 12) link_BETA1-2 : bond 0.00661 ( 2) link_BETA1-2 : angle 4.16928 ( 6) link_BETA1-4 : bond 0.00507 ( 14) link_BETA1-4 : angle 2.89378 ( 42) link_ALPHA1-3 : bond 0.01025 ( 6) link_ALPHA1-3 : angle 3.61740 ( 18) hydrogen bonds : bond 0.05595 ( 1002) hydrogen bonds : angle 4.31382 ( 2988) link_BETA1-6 : bond 0.00269 ( 4) link_BETA1-6 : angle 1.71749 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00459 (22768) covalent geometry : angle 0.60146 (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 236 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 160 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8633 (t0) REVERT: D 160 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7973 (m) REVERT: D 200 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7735 (tp30) REVERT: D 270 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: C 309 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8989 (tt) REVERT: C 346 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8779 (tp) REVERT: C 520 THR cc_start: 0.5613 (OUTLIER) cc_final: 0.5126 (p) REVERT: C 535 LYS cc_start: 0.6172 (mttt) cc_final: 0.5449 (ttpp) REVERT: C 700 ILE cc_start: 0.8373 (mt) cc_final: 0.8149 (mm) REVERT: C 780 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8691 (mp) REVERT: C 911 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8022 (ptt-90) REVERT: B 159 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (t0) REVERT: A 215 ASN cc_start: 0.6169 (m-40) cc_final: 0.5782 (p0) REVERT: A 244 PHE cc_start: 0.6892 (m-80) cc_final: 0.6582 (m-80) REVERT: A 267 MET cc_start: 0.7611 (tpp) cc_final: 0.7060 (tpp) REVERT: A 309 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8887 (tt) REVERT: A 507 MET cc_start: 0.4286 (mmm) cc_final: 0.4086 (mmm) REVERT: A 534 MET cc_start: 0.4893 (mmp) cc_final: 0.4130 (mmm) REVERT: A 535 LYS cc_start: 0.5739 (mttt) cc_final: 0.5077 (ttpp) REVERT: A 592 ILE cc_start: 0.8101 (mt) cc_final: 0.7900 (mt) REVERT: A 780 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 911 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8000 (ptt180) outliers start: 76 outliers final: 52 residues processed: 227 average time/residue: 0.3338 time to fit residues: 119.3226 Evaluate side-chains 208 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 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 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 599 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain C residue 1000 LEU 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 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 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 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 1002 ASP Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104753 restraints weight = 38681.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100628 restraints weight = 41123.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102070 restraints weight = 38183.708| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 22806 Z= 0.111 Angle : 0.557 11.072 30850 Z= 0.269 Chirality : 0.043 0.444 3492 Planarity : 0.004 0.053 3774 Dihedral : 12.355 157.482 4927 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.00 % Allowed : 16.65 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2630 helix: 1.89 (0.16), residues: 1168 sheet: 0.03 (0.30), residues: 300 loop : -0.50 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 890 HIS 0.009 0.001 HIS A 493 PHE 0.014 0.001 PHE B 25 TYR 0.016 0.001 TYR A 869 ARG 0.012 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 8) link_NAG-ASN : angle 1.34057 ( 24) link_ALPHA1-6 : bond 0.00663 ( 4) link_ALPHA1-6 : angle 1.68174 ( 12) link_BETA1-2 : bond 0.00605 ( 2) link_BETA1-2 : angle 4.21547 ( 6) link_BETA1-4 : bond 0.00614 ( 14) link_BETA1-4 : angle 2.73188 ( 42) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 3.73311 ( 18) hydrogen bonds : bond 0.04529 ( 1002) hydrogen bonds : angle 4.13234 ( 2988) link_BETA1-6 : bond 0.00119 ( 4) link_BETA1-6 : angle 1.62640 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00242 (22768) covalent geometry : angle 0.53499 (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 213 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 200 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7642 (tp30) REVERT: D 270 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: C 478 VAL cc_start: 0.2916 (OUTLIER) cc_final: 0.2701 (t) REVERT: C 520 THR cc_start: 0.5691 (OUTLIER) cc_final: 0.5287 (p) REVERT: C 535 LYS cc_start: 0.6067 (mttt) cc_final: 0.5386 (ttpp) REVERT: C 911 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8146 (ptt180) REVERT: B 159 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 203 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: B 223 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7366 (ttm-80) REVERT: A 215 ASN cc_start: 0.6230 (m-40) cc_final: 0.5975 (p0) REVERT: A 244 PHE cc_start: 0.6789 (m-80) cc_final: 0.6535 (m-80) REVERT: A 267 MET cc_start: 0.7501 (tpp) cc_final: 0.6902 (tpp) REVERT: A 386 MET cc_start: 0.7407 (mmt) cc_final: 0.7090 (mmt) REVERT: A 507 MET cc_start: 0.4411 (mmm) cc_final: 0.4116 (mmm) REVERT: A 517 ARG cc_start: 0.3509 (mtt180) cc_final: 0.2682 (ttp-170) REVERT: A 534 MET cc_start: 0.4902 (mmp) cc_final: 0.4186 (mmm) REVERT: A 535 LYS cc_start: 0.5673 (mttt) cc_final: 0.5018 (ttpp) outliers start: 45 outliers final: 27 residues processed: 202 average time/residue: 0.3363 time to fit residues: 106.1068 Evaluate side-chains 193 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE 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 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 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: 20.0000 chunk 172 optimal weight: 5.9990 chunk 192 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105205 restraints weight = 39000.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100447 restraints weight = 40641.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101896 restraints weight = 38755.259| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22806 Z= 0.113 Angle : 0.544 12.374 30850 Z= 0.262 Chirality : 0.042 0.448 3492 Planarity : 0.004 0.053 3774 Dihedral : 11.951 158.529 4926 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.73 % Allowed : 17.10 % Favored : 81.17 % 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: 1.01 (0.17), residues: 2630 helix: 1.95 (0.15), residues: 1170 sheet: -0.01 (0.29), residues: 306 loop : -0.45 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 906 HIS 0.007 0.001 HIS A 493 PHE 0.027 0.001 PHE D 25 TYR 0.021 0.001 TYR A 488 ARG 0.008 0.000 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 8) link_NAG-ASN : angle 1.32918 ( 24) link_ALPHA1-6 : bond 0.00634 ( 4) link_ALPHA1-6 : angle 1.64036 ( 12) link_BETA1-2 : bond 0.00671 ( 2) link_BETA1-2 : angle 4.12712 ( 6) link_BETA1-4 : bond 0.00610 ( 14) link_BETA1-4 : angle 2.63484 ( 42) link_ALPHA1-3 : bond 0.01047 ( 6) link_ALPHA1-3 : angle 3.74248 ( 18) hydrogen bonds : bond 0.04374 ( 1002) hydrogen bonds : angle 4.07004 ( 2988) link_BETA1-6 : bond 0.00124 ( 4) link_BETA1-6 : angle 1.59747 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00250 (22768) covalent geometry : angle 0.52257 (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 206 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (t0) REVERT: D 200 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7685 (tp30) REVERT: D 270 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: C 520 THR cc_start: 0.5641 (OUTLIER) cc_final: 0.5306 (p) REVERT: C 535 LYS cc_start: 0.6231 (mttt) cc_final: 0.5468 (ttpp) REVERT: B 203 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: B 223 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7425 (ttm-80) REVERT: A 70 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6922 (tm-30) REVERT: A 215 ASN cc_start: 0.6113 (m-40) cc_final: 0.5881 (p0) REVERT: A 244 PHE cc_start: 0.6733 (m-80) cc_final: 0.6444 (m-80) REVERT: A 267 MET cc_start: 0.7582 (tpp) cc_final: 0.6908 (tpp) REVERT: A 386 MET cc_start: 0.7121 (mmt) cc_final: 0.6905 (mmt) REVERT: A 507 MET cc_start: 0.4619 (mmm) cc_final: 0.4374 (mmm) REVERT: A 517 ARG cc_start: 0.3679 (mtt180) cc_final: 0.2858 (ttp-170) REVERT: A 534 MET cc_start: 0.4939 (mmp) cc_final: 0.4133 (mmm) REVERT: A 535 LYS cc_start: 0.5738 (mttt) cc_final: 0.5107 (ttpp) outliers start: 39 outliers final: 26 residues processed: 199 average time/residue: 0.3572 time to fit residues: 111.9645 Evaluate side-chains 182 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE 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 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 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: 9.9990 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 82 optimal weight: 0.0060 chunk 209 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.142481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103775 restraints weight = 39849.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098346 restraints weight = 34647.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099656 restraints weight = 35084.567| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 22806 Z= 0.107 Angle : 0.559 11.330 30850 Z= 0.268 Chirality : 0.042 0.439 3492 Planarity : 0.004 0.070 3774 Dihedral : 11.921 158.412 4922 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 17.72 % Favored : 80.86 % 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: 1.05 (0.17), residues: 2630 helix: 1.92 (0.15), residues: 1184 sheet: 0.14 (0.30), residues: 304 loop : -0.42 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 906 HIS 0.007 0.001 HIS A 493 PHE 0.013 0.001 PHE B 25 TYR 0.017 0.001 TYR A 869 ARG 0.009 0.000 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 8) link_NAG-ASN : angle 2.86415 ( 24) link_ALPHA1-6 : bond 0.00629 ( 4) link_ALPHA1-6 : angle 1.59845 ( 12) link_BETA1-2 : bond 0.00723 ( 2) link_BETA1-2 : angle 4.07394 ( 6) link_BETA1-4 : bond 0.00660 ( 14) link_BETA1-4 : angle 2.74579 ( 42) link_ALPHA1-3 : bond 0.00997 ( 6) link_ALPHA1-3 : angle 3.83712 ( 18) hydrogen bonds : bond 0.04130 ( 1002) hydrogen bonds : angle 4.03925 ( 2988) link_BETA1-6 : bond 0.00127 ( 4) link_BETA1-6 : angle 1.54365 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00233 (22768) covalent geometry : angle 0.53228 (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 193 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8525 (t0) REVERT: D 200 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7558 (tp30) REVERT: C 520 THR cc_start: 0.5613 (OUTLIER) cc_final: 0.5271 (p) REVERT: C 535 LYS cc_start: 0.6093 (mttt) cc_final: 0.5337 (ttpp) REVERT: C 748 MET cc_start: 0.7221 (ttt) cc_final: 0.6766 (ttt) REVERT: B 203 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: B 223 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7389 (ttm-80) REVERT: A 70 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 244 PHE cc_start: 0.6728 (m-80) cc_final: 0.6453 (m-80) REVERT: A 267 MET cc_start: 0.7584 (tpp) cc_final: 0.6842 (tpp) REVERT: A 386 MET cc_start: 0.7322 (mmt) cc_final: 0.7025 (mmt) REVERT: A 507 MET cc_start: 0.4648 (mmm) cc_final: 0.4405 (mmm) REVERT: A 517 ARG cc_start: 0.3694 (mtt180) cc_final: 0.2859 (ttp-170) REVERT: A 534 MET cc_start: 0.4930 (mmp) cc_final: 0.4130 (mmm) REVERT: A 535 LYS cc_start: 0.5773 (mttt) cc_final: 0.5153 (ttpp) outliers start: 32 outliers final: 26 residues processed: 188 average time/residue: 0.3454 time to fit residues: 101.7435 Evaluate side-chains 180 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 THR 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 1002 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 203 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 215 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101463 restraints weight = 39024.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096934 restraints weight = 47199.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098646 restraints weight = 41401.326| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 22806 Z= 0.202 Angle : 0.643 10.385 30850 Z= 0.313 Chirality : 0.045 0.418 3492 Planarity : 0.005 0.054 3774 Dihedral : 12.337 162.670 4922 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 17.72 % 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: 0.82 (0.16), residues: 2630 helix: 1.65 (0.15), residues: 1182 sheet: 0.14 (0.30), residues: 290 loop : -0.48 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 105 HIS 0.005 0.001 HIS C 685 PHE 0.026 0.002 PHE D 25 TYR 0.020 0.002 TYR D 248 ARG 0.011 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 3.05907 ( 24) link_ALPHA1-6 : bond 0.00558 ( 4) link_ALPHA1-6 : angle 1.63383 ( 12) link_BETA1-2 : bond 0.01180 ( 2) link_BETA1-2 : angle 3.91203 ( 6) link_BETA1-4 : bond 0.00593 ( 14) link_BETA1-4 : angle 2.77678 ( 42) link_ALPHA1-3 : bond 0.00990 ( 6) link_ALPHA1-3 : angle 3.93018 ( 18) hydrogen bonds : bond 0.05737 ( 1002) hydrogen bonds : angle 4.26728 ( 2988) link_BETA1-6 : bond 0.00259 ( 4) link_BETA1-6 : angle 1.67891 ( 12) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00491 (22768) covalent geometry : angle 0.61857 (30730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6741.80 seconds wall clock time: 119 minutes 3.97 seconds (7143.97 seconds total)