Starting phenix.real_space_refine on Mon Aug 25 19:33:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbf_38216/08_2025/8xbf_38216.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 19155 2.51 5 N 5026 2.21 5 O 5782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30099 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "B" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "C" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 5.82, per 1000 atoms: 0.19 Number of scatterers: 30099 At special positions: 0 Unit cell: (149.04, 159.84, 209.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 5782 8.00 N 5026 7.00 C 19155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 98 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7124 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 63 sheets defined 21.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.513A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.250A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 857 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.026A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.533A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.891A pdb=" N SER A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.110A pdb=" N VAL B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.817A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.742A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.736A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.577A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.201A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 3.834A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.848A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.535A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.648A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.953A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.533A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.449A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.648A pdb=" N SER C1147 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.620A pdb=" N ASN D 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.554A pdb=" N THR D 93 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.889A pdb=" N THR F 93 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.382A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.499A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.529A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 197 removed outlier: 5.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.567A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.979A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.575A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 656 removed outlier: 4.672A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.401A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.608A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 22 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.422A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AC7, first strand: chain 'B' and resid 203 through 205 removed outlier: 7.906A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.154A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.550A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.579A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.106A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 7.254A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 22 through 30 removed outlier: 3.781A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.648A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.182A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.777A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.484A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.753A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.650A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.635A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.712A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AF9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.140A pdb=" N GLY D 13 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 36 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D 37 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.140A pdb=" N GLY D 13 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 108 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.083A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.083A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 97 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AG6, first strand: chain 'F' and resid 14 through 15 removed outlier: 3.608A pdb=" N TYR F 36 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.387A pdb=" N ARG F 100 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 5 through 7 removed outlier: 4.230A pdb=" N ASP G 17 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL G 19 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER G 76 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE G 21 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR G 74 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS G 23 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR G 72 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.460A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2907 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: 6.65 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9699 1.35 - 1.47: 7676 1.47 - 1.59: 13263 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 30812 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA TRP G 32 " pdb=" C TRP G 32 " ideal model delta sigma weight residual 1.524 1.567 -0.043 1.47e-02 4.63e+03 8.64e+00 bond pdb=" C LEU B 223 " pdb=" N GLU B 224 " ideal model delta sigma weight residual 1.333 1.403 -0.071 2.74e-02 1.33e+03 6.65e+00 ... (remaining 30807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 41293 2.13 - 4.26: 583 4.26 - 6.39: 47 6.39 - 8.52: 5 8.52 - 10.65: 5 Bond angle restraints: 41933 Sorted by residual: angle pdb=" C TYR C1067 " pdb=" N VAL C1068 " pdb=" CA VAL C1068 " ideal model delta sigma weight residual 122.85 119.61 3.24 8.70e-01 1.32e+00 1.39e+01 angle pdb=" CA TRP G 32 " pdb=" C TRP G 32 " pdb=" N LEU G 33 " ideal model delta sigma weight residual 117.40 122.16 -4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C TYR G 94 " pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta sigma weight residual 120.82 125.79 -4.97 1.50e+00 4.44e-01 1.10e+01 angle pdb=" CA GLY A 700 " pdb=" C GLY A 700 " pdb=" N ALA A 701 " ideal model delta sigma weight residual 114.23 116.90 -2.67 8.80e-01 1.29e+00 9.21e+00 angle pdb=" CA TRP G 32 " pdb=" C TRP G 32 " pdb=" O TRP G 32 " ideal model delta sigma weight residual 120.32 117.35 2.97 1.02e+00 9.61e-01 8.49e+00 ... (remaining 41928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 17738 24.31 - 48.62: 697 48.62 - 72.93: 128 72.93 - 97.24: 24 97.24 - 121.55: 7 Dihedral angle restraints: 18594 sinusoidal: 7469 harmonic: 11125 Sorted by residual: dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA VAL B 267 " pdb=" C VAL B 267 " pdb=" N GLY B 268 " pdb=" CA GLY B 268 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA TYR G 94 " pdb=" C TYR G 94 " pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 18591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4542 0.100 - 0.200: 218 0.200 - 0.300: 0 0.300 - 0.400: 0 0.400 - 0.500: 2 Chirality restraints: 4762 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4759 not shown) Planarity restraints: 5429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO B 561 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 986 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 330 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.025 5.00e-02 4.00e+02 ... (remaining 5426 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 610 2.63 - 3.19: 28497 3.19 - 3.76: 48758 3.76 - 4.33: 67364 4.33 - 4.90: 107938 Nonbonded interactions: 253167 Sorted by model distance: nonbonded pdb=" O GLY A 496 " pdb=" OH TYR A 501 " model vdw 2.057 3.040 nonbonded pdb=" OG SER C 659 " pdb=" O THR C 696 " model vdw 2.096 3.040 nonbonded pdb=" OG SER G 63 " pdb=" O THR G 74 " model vdw 2.118 3.040 nonbonded pdb=" OG SER A 659 " pdb=" O THR A 696 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" O HIS B 66 " model vdw 2.138 3.040 ... (remaining 253162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 4.020 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.350 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 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 : 0.004 0.085 30876 Z= 0.191 Angle : 0.645 13.503 42079 Z= 0.347 Chirality : 0.045 0.500 4762 Planarity : 0.004 0.068 5411 Dihedral : 13.647 121.547 11332 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.28 % Allowed : 10.37 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3819 helix: 0.72 (0.19), residues: 753 sheet: -1.24 (0.19), residues: 677 loop : -1.39 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 61 TYR 0.018 0.001 TYR B 170 PHE 0.018 0.001 PHE A 565 TRP 0.020 0.001 TRP G 32 HIS 0.004 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00378 (30812) covalent geometry : angle 0.62909 (41933) SS BOND : bond 0.00280 ( 46) SS BOND : angle 0.98531 ( 92) hydrogen bonds : bond 0.14074 ( 1083) hydrogen bonds : angle 8.01508 ( 2907) link_NAG-ASN : bond 0.00628 ( 18) link_NAG-ASN : angle 3.88530 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 90 time to evaluate : 0.804 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: A 398 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6456 (p0) REVERT: A 465 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.3267 (tt0) REVERT: A 740 MET cc_start: 0.8386 (tpt) cc_final: 0.8046 (tpt) REVERT: A 1119 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 177 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4629 (mmp) REVERT: B 310 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6730 (ptmm) REVERT: B 508 TYR cc_start: 0.7951 (m-10) cc_final: 0.7685 (m-10) REVERT: B 573 THR cc_start: 0.0556 (OUTLIER) cc_final: -0.1868 (t) REVERT: B 727 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8794 (mm) REVERT: B 894 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7988 (mp) REVERT: C 196 ASN cc_start: 0.4667 (OUTLIER) cc_final: 0.3945 (p0) REVERT: C 258 TRP cc_start: 0.4641 (OUTLIER) cc_final: 0.1358 (p90) REVERT: C 900 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7454 (mtm) REVERT: C 1073 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6723 (mmmt) REVERT: D 37 MET cc_start: -0.3044 (OUTLIER) cc_final: -0.3275 (mtp) REVERT: E 77 SER cc_start: 0.5699 (OUTLIER) cc_final: 0.5094 (p) REVERT: F 107 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7228 (p0) outliers start: 175 outliers final: 65 residues processed: 253 average time/residue: 0.1644 time to fit residues: 69.9177 Evaluate side-chains 147 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 66 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 901 GLN A 920 GLN A1023 ASN A1054 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN B 914 ASN B1023 ASN B1054 GLN B1088 HIS C 762 GLN C 901 GLN C 913 GLN C 919 ASN C 935 GLN C 953 ASN C1054 GLN D 42 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 42 GLN G 6 GLN G 37 GLN G 38 GLN G 79 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.089646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.062054 restraints weight = 227635.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.061190 restraints weight = 208719.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.061300 restraints weight = 198992.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.061580 restraints weight = 183670.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.061794 restraints weight = 163424.473| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 30876 Z= 0.186 Angle : 0.637 12.131 42079 Z= 0.327 Chirality : 0.046 0.458 4762 Planarity : 0.005 0.061 5411 Dihedral : 9.661 107.314 4679 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.10 % Allowed : 11.79 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.13), residues: 3819 helix: 0.85 (0.19), residues: 762 sheet: -1.34 (0.18), residues: 686 loop : -1.36 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.024 0.002 TYR B 170 PHE 0.023 0.001 PHE A 559 TRP 0.015 0.001 TRP G 32 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00397 (30812) covalent geometry : angle 0.62345 (41933) SS BOND : bond 0.00477 ( 46) SS BOND : angle 1.22373 ( 92) hydrogen bonds : bond 0.05008 ( 1083) hydrogen bonds : angle 6.99991 ( 2907) link_NAG-ASN : bond 0.00585 ( 18) link_NAG-ASN : angle 3.50021 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 73 time to evaluate : 0.772 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: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: -0.1343 (OUTLIER) cc_final: -0.1574 (mptt) REVERT: A 740 MET cc_start: 0.8935 (tpt) cc_final: 0.8627 (tpt) REVERT: A 855 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 873 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6130 (t80) REVERT: B 204 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.3375 (m-80) REVERT: B 573 THR cc_start: -0.0815 (OUTLIER) cc_final: -0.2454 (t) REVERT: B 894 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7869 (mp) REVERT: C 196 ASN cc_start: 0.4901 (OUTLIER) cc_final: 0.4418 (p0) REVERT: C 258 TRP cc_start: 0.2193 (OUTLIER) cc_final: 0.0833 (p90) REVERT: C 693 ILE cc_start: 0.5188 (OUTLIER) cc_final: 0.4922 (pp) REVERT: D 37 MET cc_start: -0.2399 (OUTLIER) cc_final: -0.2825 (mtt) REVERT: D 82 PHE cc_start: 0.8735 (m-80) cc_final: 0.8459 (m-80) REVERT: E 4 MET cc_start: 0.7515 (pmm) cc_final: 0.6692 (pmm) outliers start: 136 outliers final: 74 residues processed: 201 average time/residue: 0.1628 time to fit residues: 55.0592 Evaluate side-chains 147 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 63 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 123 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 322 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 409 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.089671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.062055 restraints weight = 226512.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.061019 restraints weight = 218619.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.061303 restraints weight = 208453.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.061665 restraints weight = 184986.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.061643 restraints weight = 173703.657| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 30876 Z= 0.161 Angle : 0.606 11.652 42079 Z= 0.309 Chirality : 0.045 0.439 4762 Planarity : 0.004 0.060 5411 Dihedral : 8.975 103.769 4631 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.77 % Allowed : 12.96 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.13), residues: 3819 helix: 0.98 (0.19), residues: 762 sheet: -1.38 (0.18), residues: 701 loop : -1.36 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.020 0.002 TYR B 170 PHE 0.021 0.001 PHE A 559 TRP 0.020 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00341 (30812) covalent geometry : angle 0.59286 (41933) SS BOND : bond 0.00398 ( 46) SS BOND : angle 1.16122 ( 92) hydrogen bonds : bond 0.04601 ( 1083) hydrogen bonds : angle 6.75276 ( 2907) link_NAG-ASN : bond 0.00578 ( 18) link_NAG-ASN : angle 3.33432 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 68 time to evaluate : 0.815 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: symmetry clash REVERT: A 458 LYS cc_start: -0.1122 (OUTLIER) cc_final: -0.1351 (mptt) REVERT: A 740 MET cc_start: 0.8887 (tpt) cc_final: 0.8679 (tpt) REVERT: A 855 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 204 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.3109 (m-80) REVERT: B 206 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4700 (mmmt) REVERT: B 573 THR cc_start: -0.0857 (OUTLIER) cc_final: -0.2534 (t) REVERT: B 727 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8399 (mm) REVERT: C 18 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8019 (tp) REVERT: C 196 ASN cc_start: 0.4977 (OUTLIER) cc_final: 0.4478 (p0) REVERT: C 258 TRP cc_start: 0.2076 (OUTLIER) cc_final: 0.0874 (p90) REVERT: C 284 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6330 (m) REVERT: C 693 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4759 (pp) REVERT: D 30 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5607 (tt) REVERT: D 37 MET cc_start: -0.2078 (OUTLIER) cc_final: -0.2482 (mtt) REVERT: E 4 MET cc_start: 0.7783 (pmm) cc_final: 0.6859 (pmm) REVERT: F 37 MET cc_start: 0.7705 (mpp) cc_final: 0.7374 (mpp) REVERT: G 90 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7180 (m90) outliers start: 125 outliers final: 68 residues processed: 189 average time/residue: 0.1474 time to fit residues: 47.3704 Evaluate side-chains 143 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 61 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 362 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 450 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 52 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.093951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.083393 restraints weight = 278613.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.083972 restraints weight = 206811.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.084227 restraints weight = 175443.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.084420 restraints weight = 152383.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.084420 restraints weight = 139485.949| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 30876 Z= 0.371 Angle : 0.773 16.305 42079 Z= 0.405 Chirality : 0.050 0.417 4762 Planarity : 0.006 0.092 5411 Dihedral : 9.325 107.900 4619 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.52 % Allowed : 13.63 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.13), residues: 3819 helix: 0.69 (0.19), residues: 738 sheet: -1.70 (0.17), residues: 748 loop : -1.58 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.047 0.003 TYR B 91 PHE 0.037 0.003 PHE A 559 TRP 0.024 0.002 TRP G 32 HIS 0.007 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00804 (30812) covalent geometry : angle 0.76135 (41933) SS BOND : bond 0.00629 ( 46) SS BOND : angle 1.41198 ( 92) hydrogen bonds : bond 0.05975 ( 1083) hydrogen bonds : angle 7.28339 ( 2907) link_NAG-ASN : bond 0.00590 ( 18) link_NAG-ASN : angle 3.51756 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 68 time to evaluate : 1.163 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: A 498 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.4746 (mtm180) REVERT: A 740 MET cc_start: 0.8669 (tpt) cc_final: 0.8282 (tpt) REVERT: A 855 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 172 SER cc_start: 0.1228 (OUTLIER) cc_final: 0.0418 (t) REVERT: B 204 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.4850 (m-10) REVERT: B 277 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5388 (mm) REVERT: B 508 TYR cc_start: 0.8214 (m-10) cc_final: 0.7940 (m-10) REVERT: B 573 THR cc_start: 0.0698 (OUTLIER) cc_final: -0.1342 (t) REVERT: B 727 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8577 (mm) REVERT: C 167 THR cc_start: -0.0934 (OUTLIER) cc_final: -0.2014 (t) REVERT: C 196 ASN cc_start: 0.4656 (OUTLIER) cc_final: 0.3964 (p0) REVERT: C 242 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7515 (tt) REVERT: C 258 TRP cc_start: 0.4184 (OUTLIER) cc_final: 0.1244 (p90) REVERT: C 284 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6556 (m) REVERT: C 559 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.5410 (t80) REVERT: C 693 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6114 (pp) REVERT: D 37 MET cc_start: -0.2243 (OUTLIER) cc_final: -0.2581 (mtt) REVERT: E 4 MET cc_start: 0.6262 (pmm) cc_final: 0.5479 (pmm) REVERT: G 90 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6635 (m90) outliers start: 150 outliers final: 85 residues processed: 212 average time/residue: 0.1583 time to fit residues: 56.0134 Evaluate side-chains 164 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 63 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 106 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 282 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 351 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 42 GLN E 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.088738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.061276 restraints weight = 228029.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.060837 restraints weight = 213513.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.060875 restraints weight = 197371.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.062331 restraints weight = 180522.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.061917 restraints weight = 158531.383| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30876 Z= 0.130 Angle : 0.607 12.603 42079 Z= 0.308 Chirality : 0.046 0.413 4762 Planarity : 0.004 0.060 5411 Dihedral : 8.624 101.189 4617 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.14 % Allowed : 14.95 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 3819 helix: 1.06 (0.19), residues: 744 sheet: -1.58 (0.18), residues: 733 loop : -1.40 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1000 TYR 0.014 0.001 TYR A 873 PHE 0.018 0.001 PHE A 559 TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (30812) covalent geometry : angle 0.59243 (41933) SS BOND : bond 0.00462 ( 46) SS BOND : angle 1.63011 ( 92) hydrogen bonds : bond 0.04452 ( 1083) hydrogen bonds : angle 6.70411 ( 2907) link_NAG-ASN : bond 0.00547 ( 18) link_NAG-ASN : angle 3.18269 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 68 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.0592 (OUTLIER) cc_final: 0.0240 (tp) REVERT: A 282 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7299 (m110) REVERT: A 855 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: B 133 PHE cc_start: -0.1052 (OUTLIER) cc_final: -0.1307 (t80) REVERT: B 204 TYR cc_start: 0.4837 (OUTLIER) cc_final: 0.3233 (m-80) REVERT: B 371 PHE cc_start: -0.1620 (OUTLIER) cc_final: -0.1852 (t80) REVERT: B 573 THR cc_start: -0.1233 (OUTLIER) cc_final: -0.2735 (t) REVERT: B 727 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8330 (mm) REVERT: C 196 ASN cc_start: 0.4938 (OUTLIER) cc_final: 0.4159 (p0) REVERT: C 218 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: C 242 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7428 (tt) REVERT: C 258 TRP cc_start: 0.2138 (OUTLIER) cc_final: 0.0882 (p90) REVERT: C 284 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.6265 (m) REVERT: C 693 ILE cc_start: 0.5063 (OUTLIER) cc_final: 0.4855 (pp) REVERT: D 37 MET cc_start: -0.0792 (mmt) cc_final: -0.1074 (mtt) REVERT: E 4 MET cc_start: 0.8108 (pmm) cc_final: 0.7245 (pmm) REVERT: G 90 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.6832 (m90) outliers start: 104 outliers final: 63 residues processed: 167 average time/residue: 0.1616 time to fit residues: 45.8411 Evaluate side-chains 141 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 63 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 263 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 261 optimal weight: 50.0000 chunk 170 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 374 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN D 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.088283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.061076 restraints weight = 227518.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.060297 restraints weight = 216507.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.060610 restraints weight = 200435.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.060900 restraints weight = 177340.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.061210 restraints weight = 158014.362| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30876 Z= 0.158 Angle : 0.601 11.631 42079 Z= 0.307 Chirality : 0.045 0.403 4762 Planarity : 0.005 0.063 5411 Dihedral : 8.360 99.678 4599 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.23 % Allowed : 15.25 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.13), residues: 3819 helix: 1.11 (0.19), residues: 747 sheet: -1.55 (0.17), residues: 790 loop : -1.38 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 61 TYR 0.019 0.001 TYR B 170 PHE 0.026 0.001 PHE B 168 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00341 (30812) covalent geometry : angle 0.58888 (41933) SS BOND : bond 0.00428 ( 46) SS BOND : angle 1.38203 ( 92) hydrogen bonds : bond 0.04498 ( 1083) hydrogen bonds : angle 6.63328 ( 2907) link_NAG-ASN : bond 0.00525 ( 18) link_NAG-ASN : angle 3.04107 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 66 time to evaluate : 1.162 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: A 110 LEU cc_start: 0.0647 (OUTLIER) cc_final: 0.0277 (tp) REVERT: A 282 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7354 (m110) REVERT: A 498 ARG cc_start: 0.5222 (OUTLIER) cc_final: 0.4901 (mtm180) REVERT: A 855 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: B 204 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.3268 (m-80) REVERT: B 371 PHE cc_start: -0.1636 (OUTLIER) cc_final: -0.1840 (t80) REVERT: B 573 THR cc_start: -0.1132 (OUTLIER) cc_final: -0.2802 (t) REVERT: B 727 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8356 (mm) REVERT: C 167 THR cc_start: -0.1449 (OUTLIER) cc_final: -0.2454 (t) REVERT: C 196 ASN cc_start: 0.5229 (OUTLIER) cc_final: 0.4720 (p0) REVERT: C 218 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6345 (mt0) REVERT: C 242 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7427 (tt) REVERT: C 258 TRP cc_start: 0.2281 (OUTLIER) cc_final: 0.0865 (p90) REVERT: C 284 THR cc_start: 0.6586 (OUTLIER) cc_final: 0.6259 (m) REVERT: C 693 ILE cc_start: 0.5183 (OUTLIER) cc_final: 0.4957 (pp) REVERT: D 37 MET cc_start: -0.0053 (mmt) cc_final: -0.0441 (mtt) REVERT: E 4 MET cc_start: 0.8202 (pmm) cc_final: 0.7703 (pmm) REVERT: E 90 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7460 (p-80) REVERT: G 90 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.6797 (m90) outliers start: 107 outliers final: 70 residues processed: 169 average time/residue: 0.1821 time to fit residues: 52.6349 Evaluate side-chains 152 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 65 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.0060 chunk 186 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 207 HIS D 42 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.088378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.061172 restraints weight = 227049.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.060938 restraints weight = 201230.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.060857 restraints weight = 186404.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.060943 restraints weight = 192918.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.061112 restraints weight = 173747.251| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30876 Z= 0.139 Angle : 0.580 11.518 42079 Z= 0.294 Chirality : 0.045 0.386 4762 Planarity : 0.004 0.059 5411 Dihedral : 8.114 97.682 4595 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.04 % Allowed : 15.44 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 3819 helix: 1.21 (0.19), residues: 747 sheet: -1.52 (0.17), residues: 784 loop : -1.28 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 61 TYR 0.029 0.001 TYR B 508 PHE 0.021 0.001 PHE B 168 TRP 0.018 0.001 TRP C 436 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (30812) covalent geometry : angle 0.56866 (41933) SS BOND : bond 0.00315 ( 46) SS BOND : angle 1.29546 ( 92) hydrogen bonds : bond 0.04274 ( 1083) hydrogen bonds : angle 6.45276 ( 2907) link_NAG-ASN : bond 0.00490 ( 18) link_NAG-ASN : angle 2.92047 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 65 time to evaluate : 1.200 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: symmetry clash REVERT: A 110 LEU cc_start: 0.0641 (OUTLIER) cc_final: 0.0329 (tp) REVERT: A 282 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7386 (m110) REVERT: A 855 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: B 133 PHE cc_start: -0.1110 (OUTLIER) cc_final: -0.1370 (t80) REVERT: B 204 TYR cc_start: 0.4949 (OUTLIER) cc_final: 0.3098 (m-80) REVERT: B 371 PHE cc_start: -0.1100 (OUTLIER) cc_final: -0.1435 (t80) REVERT: B 573 THR cc_start: -0.1219 (OUTLIER) cc_final: -0.2924 (t) REVERT: B 727 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7966 (mm) REVERT: B 900 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6966 (mtm) REVERT: C 167 THR cc_start: -0.1489 (OUTLIER) cc_final: -0.2495 (t) REVERT: C 196 ASN cc_start: 0.5346 (OUTLIER) cc_final: 0.4853 (p0) REVERT: C 218 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6246 (mt0) REVERT: C 258 TRP cc_start: 0.2158 (OUTLIER) cc_final: 0.0890 (p90) REVERT: C 284 THR cc_start: 0.6541 (OUTLIER) cc_final: 0.6202 (m) REVERT: C 693 ILE cc_start: 0.5109 (OUTLIER) cc_final: 0.4879 (pp) REVERT: D 37 MET cc_start: 0.0014 (mmt) cc_final: -0.0371 (mtt) REVERT: E 4 MET cc_start: 0.8409 (pmm) cc_final: 0.8060 (pmm) REVERT: E 90 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7485 (p-80) REVERT: G 90 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.6823 (m90) outliers start: 101 outliers final: 65 residues processed: 164 average time/residue: 0.1857 time to fit residues: 51.3001 Evaluate side-chains 144 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 62 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 68 optimal weight: 0.0270 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 377 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 42 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.087586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.060078 restraints weight = 226297.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.059695 restraints weight = 217550.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.059599 restraints weight = 198659.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.059876 restraints weight = 189235.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.060186 restraints weight = 169824.840| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 30876 Z= 0.192 Angle : 0.622 11.003 42079 Z= 0.319 Chirality : 0.046 0.374 4762 Planarity : 0.005 0.059 5411 Dihedral : 8.235 99.944 4592 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.04 % Allowed : 16.01 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.13), residues: 3819 helix: 1.17 (0.19), residues: 747 sheet: -1.61 (0.17), residues: 779 loop : -1.33 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 61 TYR 0.033 0.002 TYR A 873 PHE 0.021 0.001 PHE A 559 TRP 0.013 0.001 TRP C1102 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00417 (30812) covalent geometry : angle 0.61131 (41933) SS BOND : bond 0.00349 ( 46) SS BOND : angle 1.32021 ( 92) hydrogen bonds : bond 0.04634 ( 1083) hydrogen bonds : angle 6.59870 ( 2907) link_NAG-ASN : bond 0.00518 ( 18) link_NAG-ASN : angle 2.93766 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 66 time to evaluate : 1.139 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: A 110 LEU cc_start: 0.0773 (OUTLIER) cc_final: 0.0473 (tp) REVERT: A 282 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7443 (m110) REVERT: A 855 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: B 133 PHE cc_start: -0.1155 (OUTLIER) cc_final: -0.1389 (t80) REVERT: B 204 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.3525 (m-80) REVERT: B 371 PHE cc_start: -0.0256 (OUTLIER) cc_final: -0.0823 (t80) REVERT: B 573 THR cc_start: -0.0587 (OUTLIER) cc_final: -0.2069 (t) REVERT: B 727 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 900 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7262 (mtm) REVERT: C 167 THR cc_start: -0.1438 (OUTLIER) cc_final: -0.2427 (t) REVERT: C 196 ASN cc_start: 0.5797 (OUTLIER) cc_final: 0.5328 (p0) REVERT: C 218 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6484 (mt0) REVERT: C 238 PHE cc_start: -0.0864 (OUTLIER) cc_final: -0.1771 (p90) REVERT: C 258 TRP cc_start: 0.2124 (OUTLIER) cc_final: 0.0813 (p90) REVERT: C 693 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4928 (pp) REVERT: D 37 MET cc_start: 0.0554 (mmt) cc_final: -0.0095 (mtm) REVERT: D 82 PHE cc_start: 0.8705 (m-80) cc_final: 0.8450 (m-80) REVERT: E 4 MET cc_start: 0.8543 (pmm) cc_final: 0.7877 (pmm) REVERT: G 90 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.6879 (m90) outliers start: 101 outliers final: 70 residues processed: 161 average time/residue: 0.1560 time to fit residues: 42.5797 Evaluate side-chains 149 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 63 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 137 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN D 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.087544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.060363 restraints weight = 227668.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.059922 restraints weight = 217320.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.060014 restraints weight = 200869.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.060159 restraints weight = 192106.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.060440 restraints weight = 169252.774| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30876 Z= 0.157 Angle : 0.596 11.229 42079 Z= 0.302 Chirality : 0.045 0.368 4762 Planarity : 0.004 0.061 5411 Dihedral : 8.085 99.548 4592 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.86 % Allowed : 16.16 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.13), residues: 3819 helix: 1.22 (0.19), residues: 747 sheet: -1.54 (0.17), residues: 773 loop : -1.29 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 61 TYR 0.028 0.001 TYR A 873 PHE 0.015 0.001 PHE A 559 TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (30812) covalent geometry : angle 0.58551 (41933) SS BOND : bond 0.00308 ( 46) SS BOND : angle 1.21842 ( 92) hydrogen bonds : bond 0.04404 ( 1083) hydrogen bonds : angle 6.49340 ( 2907) link_NAG-ASN : bond 0.00493 ( 18) link_NAG-ASN : angle 2.88209 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 63 time to evaluate : 1.221 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: A 110 LEU cc_start: 0.0876 (OUTLIER) cc_final: 0.0578 (tp) REVERT: A 282 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7477 (m110) REVERT: A 855 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: A 1050 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7435 (ptp) REVERT: B 133 PHE cc_start: -0.1030 (OUTLIER) cc_final: -0.1287 (t80) REVERT: B 204 TYR cc_start: 0.5073 (OUTLIER) cc_final: 0.3195 (m-80) REVERT: B 371 PHE cc_start: -0.0319 (OUTLIER) cc_final: -0.0817 (t80) REVERT: B 573 THR cc_start: -0.1155 (OUTLIER) cc_final: -0.2664 (t) REVERT: B 727 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 900 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7285 (mtm) REVERT: C 167 THR cc_start: -0.1829 (OUTLIER) cc_final: -0.2775 (t) REVERT: C 196 ASN cc_start: 0.5974 (OUTLIER) cc_final: 0.5578 (p0) REVERT: C 218 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6627 (mt0) REVERT: C 238 PHE cc_start: -0.1091 (OUTLIER) cc_final: -0.1935 (p90) REVERT: C 258 TRP cc_start: 0.2054 (OUTLIER) cc_final: 0.0859 (p90) REVERT: C 693 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4934 (pp) REVERT: D 22 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.6367 (mmm160) REVERT: D 37 MET cc_start: 0.0468 (mmt) cc_final: -0.0026 (mtt) REVERT: E 4 MET cc_start: 0.8596 (pmm) cc_final: 0.7994 (pmm) REVERT: G 50 LYS cc_start: 0.7253 (pttt) cc_final: 0.6334 (ptpp) REVERT: G 90 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.6561 (p-80) outliers start: 95 outliers final: 66 residues processed: 153 average time/residue: 0.1694 time to fit residues: 44.3668 Evaluate side-chains 146 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 63 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 188 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN F 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.086928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.060009 restraints weight = 226179.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.059389 restraints weight = 211555.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.059353 restraints weight = 210130.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.059670 restraints weight = 187599.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.059935 restraints weight = 164358.161| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30876 Z= 0.200 Angle : 0.631 11.779 42079 Z= 0.325 Chirality : 0.046 0.359 4762 Planarity : 0.005 0.062 5411 Dihedral : 8.251 102.552 4591 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.56 % Allowed : 16.55 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.13), residues: 3819 helix: 1.13 (0.19), residues: 744 sheet: -1.64 (0.17), residues: 773 loop : -1.35 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.031 0.002 TYR A 873 PHE 0.028 0.002 PHE A 347 TRP 0.012 0.001 TRP C1102 HIS 0.007 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00434 (30812) covalent geometry : angle 0.62025 (41933) SS BOND : bond 0.00468 ( 46) SS BOND : angle 1.33022 ( 92) hydrogen bonds : bond 0.04728 ( 1083) hydrogen bonds : angle 6.65599 ( 2907) link_NAG-ASN : bond 0.00510 ( 18) link_NAG-ASN : angle 2.92775 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 66 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.0858 (OUTLIER) cc_final: -0.0029 (tt) REVERT: A 282 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7486 (m110) REVERT: A 855 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7214 (m-10) REVERT: A 1050 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7466 (ptp) REVERT: B 133 PHE cc_start: -0.0893 (OUTLIER) cc_final: -0.1162 (t80) REVERT: B 204 TYR cc_start: 0.5600 (OUTLIER) cc_final: 0.3660 (m-80) REVERT: B 512 VAL cc_start: -0.2489 (OUTLIER) cc_final: -0.2931 (m) REVERT: B 573 THR cc_start: -0.0507 (OUTLIER) cc_final: -0.2002 (t) REVERT: B 727 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8406 (mm) REVERT: B 900 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7559 (mtm) REVERT: C 167 THR cc_start: -0.1441 (OUTLIER) cc_final: -0.2481 (t) REVERT: C 196 ASN cc_start: 0.5945 (OUTLIER) cc_final: 0.5522 (p0) REVERT: C 218 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6769 (mt0) REVERT: C 238 PHE cc_start: -0.0722 (OUTLIER) cc_final: -0.1618 (p90) REVERT: C 258 TRP cc_start: 0.2405 (OUTLIER) cc_final: 0.1042 (p90) REVERT: C 693 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4929 (pp) REVERT: D 37 MET cc_start: 0.0584 (mmt) cc_final: 0.0064 (mtt) REVERT: E 4 MET cc_start: 0.8710 (pmm) cc_final: 0.8024 (pmm) REVERT: G 90 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.6722 (m90) outliers start: 85 outliers final: 64 residues processed: 145 average time/residue: 0.1556 time to fit residues: 38.9684 Evaluate side-chains 145 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 64 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 223 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 263 optimal weight: 40.0000 chunk 262 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 266 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 chunk 320 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN B 121 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN D 42 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.087474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.060746 restraints weight = 228306.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.060153 restraints weight = 224440.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.060409 restraints weight = 201030.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.060554 restraints weight = 186195.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.060981 restraints weight = 165709.672| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30876 Z= 0.131 Angle : 0.588 11.625 42079 Z= 0.297 Chirality : 0.045 0.358 4762 Planarity : 0.004 0.059 5411 Dihedral : 8.028 101.966 4588 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.38 % Allowed : 16.85 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.13), residues: 3819 helix: 1.27 (0.19), residues: 744 sheet: -1.53 (0.17), residues: 737 loop : -1.26 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 100 TYR 0.020 0.001 TYR A 873 PHE 0.017 0.001 PHE A 347 TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00281 (30812) covalent geometry : angle 0.57765 (41933) SS BOND : bond 0.00320 ( 46) SS BOND : angle 1.29335 ( 92) hydrogen bonds : bond 0.04212 ( 1083) hydrogen bonds : angle 6.44028 ( 2907) link_NAG-ASN : bond 0.00468 ( 18) link_NAG-ASN : angle 2.77410 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7466.07 seconds wall clock time: 129 minutes 0.15 seconds (7740.15 seconds total)