Starting phenix.real_space_refine on Thu Jun 26 04:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbf_38216/06_2025/8xbf_38216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbf_38216/06_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_38216/06_2025/8xbf_38216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbf_38216/06_2025/8xbf_38216.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbf_38216/06_2025/8xbf_38216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbf_38216/06_2025/8xbf_38216.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 1.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.80, per 1000 atoms: 0.56 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: 6.60 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 4.02 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: 12.92 Time building geometry restraints manager: 7.93 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: 0.08 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: 3.170 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: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 64.920 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (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 TRP 0.020 0.001 TRP G 32 HIS 0.004 0.001 HIS G 90 PHE 0.018 0.001 PHE A 565 TYR 0.018 0.001 TYR B 170 ARG 0.004 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 18) link_NAG-ASN : angle 3.88530 ( 54) hydrogen bonds : bond 0.14074 ( 1083) hydrogen bonds : angle 8.01508 ( 2907) SS BOND : bond 0.00280 ( 46) SS BOND : angle 0.98531 ( 92) covalent geometry : bond 0.00378 (30812) covalent geometry : angle 0.62909 (41933) *********************** 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 : 3.281 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: symmetry clash REVERT: A 365 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6372 (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: 0.7993 (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: 0.8796 (mm) REVERT: B 894 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7987 (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: 0.1359 (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: 0.5096 (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: 0.3907 time to fit residues: 165.2728 Evaluate side-chains 148 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 67 time to evaluate : 3.090 ------------------------------------------------------------------------------- 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 319 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 158 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 343 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1023 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.061806 restraints weight = 225311.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.061381 restraints weight = 206485.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.061118 restraints weight = 206001.549| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 30876 Z= 0.181 Angle : 0.634 12.032 42079 Z= 0.324 Chirality : 0.046 0.460 4762 Planarity : 0.005 0.062 5411 Dihedral : 9.611 106.366 4679 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.25 % Allowed : 11.49 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3819 helix: 0.82 (0.19), residues: 768 sheet: -1.34 (0.18), residues: 686 loop : -1.36 (0.12), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.005 0.001 HIS A1058 PHE 0.023 0.001 PHE A 559 TYR 0.024 0.002 TYR B 170 ARG 0.008 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 18) link_NAG-ASN : angle 3.48648 ( 54) hydrogen bonds : bond 0.04922 ( 1083) hydrogen bonds : angle 6.94955 ( 2907) SS BOND : bond 0.00400 ( 46) SS BOND : angle 1.18647 ( 92) covalent geometry : bond 0.00388 (30812) covalent geometry : angle 0.61999 (41933) *********************** 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 215 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 74 time to evaluate : 4.459 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: A 458 LYS cc_start: -0.1310 (OUTLIER) cc_final: -0.1537 (mptt) REVERT: A 740 MET cc_start: 0.8948 (tpt) cc_final: 0.8651 (tpt) REVERT: A 855 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: A 873 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.6110 (t80) REVERT: B 204 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.3302 (m-80) REVERT: B 573 THR cc_start: -0.0947 (OUTLIER) cc_final: -0.2528 (t) REVERT: B 894 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7816 (mp) REVERT: C 196 ASN cc_start: 0.4931 (OUTLIER) cc_final: 0.4475 (p0) REVERT: C 258 TRP cc_start: 0.1950 (OUTLIER) cc_final: 0.0690 (p90) REVERT: C 284 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6412 (m) REVERT: C 693 ILE cc_start: 0.5151 (OUTLIER) cc_final: 0.4893 (pp) REVERT: D 37 MET cc_start: -0.2320 (OUTLIER) cc_final: -0.2760 (mtt) REVERT: D 82 PHE cc_start: 0.8759 (m-80) cc_final: 0.8495 (m-80) REVERT: E 4 MET cc_start: 0.7688 (pmm) cc_final: 0.6829 (pmm) outliers start: 141 outliers final: 77 residues processed: 206 average time/residue: 0.4563 time to fit residues: 161.0369 Evaluate side-chains 150 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 62 time to evaluate : 3.162 ------------------------------------------------------------------------------- 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 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 599 THR Chi-restraints excluded: chain B residue 615 VAL 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 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 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 18 ARG 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 4 MET 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 148 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 374 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 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 218 GLN B 370 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** 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 = 0.4694 r_free = 0.4694 target = 0.088774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.060598 restraints weight = 225645.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.060610 restraints weight = 204895.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.060373 restraints weight = 195180.045| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 30876 Z= 0.227 Angle : 0.661 11.787 42079 Z= 0.340 Chirality : 0.047 0.429 4762 Planarity : 0.005 0.074 5411 Dihedral : 9.234 106.176 4637 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.07 % Allowed : 13.69 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3819 helix: 0.93 (0.19), residues: 744 sheet: -1.58 (0.18), residues: 738 loop : -1.45 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 436 HIS 0.005 0.001 HIS A1058 PHE 0.028 0.002 PHE A 559 TYR 0.030 0.002 TYR B 170 ARG 0.011 0.001 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 18) link_NAG-ASN : angle 3.41359 ( 54) hydrogen bonds : bond 0.05102 ( 1083) hydrogen bonds : angle 6.97118 ( 2907) SS BOND : bond 0.00392 ( 46) SS BOND : angle 1.20341 ( 92) covalent geometry : bond 0.00489 (30812) covalent geometry : angle 0.64800 (41933) *********************** 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 204 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 69 time to evaluate : 4.020 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 855 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 133 PHE cc_start: 0.0083 (OUTLIER) cc_final: -0.0147 (t80) REVERT: B 172 SER cc_start: -0.1811 (OUTLIER) cc_final: -0.2170 (t) REVERT: B 204 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.3594 (m-80) REVERT: B 206 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4774 (mmmt) REVERT: B 573 THR cc_start: -0.0412 (OUTLIER) cc_final: -0.2041 (t) REVERT: B 654 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: B 727 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8277 (mm) REVERT: C 18 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 196 ASN cc_start: 0.5064 (OUTLIER) cc_final: 0.4524 (p0) REVERT: C 258 TRP cc_start: 0.2002 (OUTLIER) cc_final: 0.0824 (p90) REVERT: C 284 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6585 (m) REVERT: C 693 ILE cc_start: 0.5102 (OUTLIER) cc_final: 0.4838 (pp) REVERT: C 1073 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.7008 (tmtt) REVERT: D 37 MET cc_start: -0.1752 (OUTLIER) cc_final: -0.2196 (mtt) REVERT: E 4 MET cc_start: 0.8017 (pmm) cc_final: 0.7082 (pmm) REVERT: G 90 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7128 (m90) outliers start: 135 outliers final: 76 residues processed: 197 average time/residue: 0.5937 time to fit residues: 202.5702 Evaluate side-chains 155 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 63 time to evaluate : 7.709 ------------------------------------------------------------------------------- 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 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 A residue 1126 CYS Chi-restraints excluded: chain B residue 47 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 206 LYS Chi-restraints excluded: chain B residue 227 VAL 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 501 TYR 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 654 GLU 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 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 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 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 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 147 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 259 optimal weight: 30.0000 chunk 335 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 333 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 357 optimal weight: 0.0000 overall best weight: 1.1824 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 146 HIS C 901 GLN D 42 GLN D 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.089334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.061906 restraints weight = 227543.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.061088 restraints weight = 214606.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.061406 restraints weight = 205772.843| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30876 Z= 0.130 Angle : 0.586 10.969 42079 Z= 0.297 Chirality : 0.045 0.421 4762 Planarity : 0.004 0.059 5411 Dihedral : 8.673 100.587 4622 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.71 % Allowed : 13.99 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3819 helix: 1.11 (0.19), residues: 747 sheet: -1.48 (0.18), residues: 708 loop : -1.33 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE A 559 TYR 0.021 0.001 TYR A 873 ARG 0.005 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 18) link_NAG-ASN : angle 3.09574 ( 54) hydrogen bonds : bond 0.04362 ( 1083) hydrogen bonds : angle 6.59904 ( 2907) SS BOND : bond 0.00286 ( 46) SS BOND : angle 1.08595 ( 92) covalent geometry : bond 0.00275 (30812) covalent geometry : angle 0.57462 (41933) *********************** 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 192 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 69 time to evaluate : 3.169 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 855 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7269 (m-10) REVERT: B 204 TYR cc_start: 0.5152 (OUTLIER) cc_final: 0.3132 (m-80) REVERT: B 573 THR cc_start: -0.1151 (OUTLIER) cc_final: -0.2592 (t) REVERT: B 727 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 900 MET cc_start: 0.7663 (mtp) cc_final: 0.7123 (mtm) REVERT: C 18 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7926 (tp) REVERT: C 23 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C 196 ASN cc_start: 0.5224 (OUTLIER) cc_final: 0.4700 (p0) REVERT: C 242 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7554 (tt) REVERT: C 258 TRP cc_start: 0.2218 (OUTLIER) cc_final: 0.0989 (p90) REVERT: C 693 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.4988 (pp) REVERT: D 37 MET cc_start: -0.1067 (OUTLIER) cc_final: -0.1484 (mtp) REVERT: E 4 MET cc_start: 0.7878 (pmm) cc_final: 0.6911 (pmm) REVERT: G 90 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7162 (m90) outliers start: 123 outliers final: 73 residues processed: 187 average time/residue: 0.4119 time to fit residues: 130.3578 Evaluate side-chains 147 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 62 time to evaluate : 4.169 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 427 ASP 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 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 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 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 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 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 18 LEU Chi-restraints excluded: chain C residue 23 GLN 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 242 LEU 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 367 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 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 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 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 135 optimal weight: 0.0040 chunk 201 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 355 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.089563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.061972 restraints weight = 225252.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.061520 restraints weight = 208163.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.061479 restraints weight = 194950.793| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30876 Z= 0.120 Angle : 0.567 12.712 42079 Z= 0.286 Chirality : 0.045 0.408 4762 Planarity : 0.004 0.057 5411 Dihedral : 8.331 97.558 4618 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.23 % Allowed : 14.53 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3819 helix: 1.22 (0.19), residues: 747 sheet: -1.42 (0.18), residues: 724 loop : -1.26 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.023 0.001 PHE D 82 TYR 0.020 0.001 TYR B 508 ARG 0.004 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 18) link_NAG-ASN : angle 2.92642 ( 54) hydrogen bonds : bond 0.04154 ( 1083) hydrogen bonds : angle 6.38556 ( 2907) SS BOND : bond 0.00307 ( 46) SS BOND : angle 1.37377 ( 92) covalent geometry : bond 0.00257 (30812) covalent geometry : angle 0.55492 (41933) *********************** 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: 107 poor density : 65 time to evaluate : 3.395 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: symmetry clash REVERT: A 110 LEU cc_start: 0.0469 (OUTLIER) cc_final: -0.0053 (tp) REVERT: A 855 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: A 1106 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: B 204 TYR cc_start: 0.4757 (OUTLIER) cc_final: 0.2851 (m-80) REVERT: B 573 THR cc_start: -0.1455 (OUTLIER) cc_final: -0.2852 (t) REVERT: B 727 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8412 (mm) REVERT: C 18 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7871 (tp) REVERT: C 196 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.4683 (p0) REVERT: C 218 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5828 (mt0) REVERT: C 258 TRP cc_start: 0.2043 (OUTLIER) cc_final: 0.0936 (p90) REVERT: C 693 ILE cc_start: 0.5057 (OUTLIER) cc_final: 0.4828 (pp) REVERT: D 37 MET cc_start: -0.0602 (mmt) cc_final: -0.0963 (mtt) REVERT: E 4 MET cc_start: 0.8305 (pmm) cc_final: 0.7679 (pmm) REVERT: E 33 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3703 (tp) REVERT: G 50 LYS cc_start: 0.6113 (pttt) cc_final: 0.5132 (ptpp) REVERT: G 90 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7064 (m90) outliers start: 107 outliers final: 71 residues processed: 171 average time/residue: 0.3985 time to fit residues: 115.4741 Evaluate side-chains 145 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 61 time to evaluate : 3.277 ------------------------------------------------------------------------------- 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 294 ASP Chi-restraints excluded: chain A residue 440 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 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 A residue 1122 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 501 TYR 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 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 18 LEU 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 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 367 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 C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 33 LEU 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 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 61 ARG Chi-restraints excluded: chain G residue 88 CYS 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 1 optimal weight: 9.9990 chunk 5 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 335 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 226 optimal weight: 0.3980 chunk 374 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 901 GLN D 42 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.088618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.060969 restraints weight = 227462.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.060566 restraints weight = 213228.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.060525 restraints weight = 201103.468| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 30876 Z= 0.179 Angle : 0.597 11.906 42079 Z= 0.304 Chirality : 0.045 0.395 4762 Planarity : 0.005 0.071 5411 Dihedral : 8.385 98.292 4608 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.20 % Allowed : 14.92 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3819 helix: 1.22 (0.19), residues: 747 sheet: -1.50 (0.18), residues: 754 loop : -1.30 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS B 505 PHE 0.027 0.001 PHE B 168 TYR 0.024 0.002 TYR B 170 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 18) link_NAG-ASN : angle 2.96344 ( 54) hydrogen bonds : bond 0.04499 ( 1083) hydrogen bonds : angle 6.47154 ( 2907) SS BOND : bond 0.00354 ( 46) SS BOND : angle 1.19734 ( 92) covalent geometry : bond 0.00387 (30812) covalent geometry : angle 0.58614 (41933) *********************** 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 171 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 65 time to evaluate : 3.208 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 110 LEU cc_start: 0.0315 (OUTLIER) cc_final: 0.0020 (tp) REVERT: A 855 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: B 172 SER cc_start: -0.1568 (OUTLIER) cc_final: -0.1869 (t) REVERT: B 204 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.3219 (m-80) REVERT: B 573 THR cc_start: -0.1083 (OUTLIER) cc_final: -0.2657 (t) REVERT: B 727 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8407 (mm) REVERT: B 1139 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7863 (p0) REVERT: C 18 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 167 THR cc_start: -0.1377 (OUTLIER) cc_final: -0.2376 (t) REVERT: C 196 ASN cc_start: 0.5342 (OUTLIER) cc_final: 0.4778 (p0) REVERT: C 218 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6239 (mt0) REVERT: C 258 TRP cc_start: 0.2099 (OUTLIER) cc_final: 0.0922 (p90) REVERT: C 284 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.6346 (m) REVERT: C 693 ILE cc_start: 0.5099 (OUTLIER) cc_final: 0.4873 (pp) REVERT: D 37 MET cc_start: -0.0463 (mmt) cc_final: -0.1031 (mtm) REVERT: E 4 MET cc_start: 0.8391 (pmm) cc_final: 0.7768 (pmm) REVERT: F 85 MET cc_start: 0.5967 (mmt) cc_final: 0.5693 (mmp) REVERT: G 90 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.6935 (m90) outliers start: 106 outliers final: 71 residues processed: 170 average time/residue: 0.4321 time to fit residues: 124.8764 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 : 3.106 ------------------------------------------------------------------------------- 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 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 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 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 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 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 501 TYR 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 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 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 36 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 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 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 C residue 1129 VAL 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 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 61 ARG Chi-restraints excluded: chain G residue 88 CYS 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 16 optimal weight: 8.9990 chunk 138 optimal weight: 0.2980 chunk 374 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 312 optimal weight: 0.5980 chunk 9 optimal weight: 0.0030 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1106 GLN ** B 52 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4733 r_free = 0.4733 target = 0.089599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.061838 restraints weight = 226471.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.061474 restraints weight = 212128.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.061463 restraints weight = 196355.639| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30876 Z= 0.112 Angle : 0.562 12.640 42079 Z= 0.282 Chirality : 0.044 0.387 4762 Planarity : 0.004 0.070 5411 Dihedral : 7.885 94.720 4594 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3819 helix: 1.41 (0.19), residues: 729 sheet: -1.42 (0.18), residues: 733 loop : -1.14 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.007 0.001 HIS C1048 PHE 0.022 0.001 PHE B 168 TYR 0.028 0.001 TYR B 508 ARG 0.007 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 18) link_NAG-ASN : angle 2.84391 ( 54) hydrogen bonds : bond 0.04000 ( 1083) hydrogen bonds : angle 6.21020 ( 2907) SS BOND : bond 0.00291 ( 46) SS BOND : angle 1.13352 ( 92) covalent geometry : bond 0.00237 (30812) covalent geometry : angle 0.55094 (41933) *********************** 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 152 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 66 time to evaluate : 3.425 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 110 LEU cc_start: 0.0648 (OUTLIER) cc_final: 0.0372 (tp) REVERT: A 855 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: B 204 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.2601 (m-80) REVERT: B 727 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8168 (mm) REVERT: B 900 MET cc_start: 0.7115 (mtp) cc_final: 0.6846 (mtt) REVERT: C 18 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7759 (tp) REVERT: C 167 THR cc_start: -0.1630 (OUTLIER) cc_final: -0.2598 (t) REVERT: C 196 ASN cc_start: 0.5218 (OUTLIER) cc_final: 0.4725 (p0) REVERT: C 218 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5903 (mt0) REVERT: C 258 TRP cc_start: 0.2063 (OUTLIER) cc_final: 0.0843 (p90) REVERT: D 37 MET cc_start: -0.0556 (mmt) cc_final: -0.0909 (mtt) REVERT: E 4 MET cc_start: 0.8417 (pmm) cc_final: 0.7973 (pmm) REVERT: G 90 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.6982 (m90) outliers start: 86 outliers final: 57 residues processed: 149 average time/residue: 0.3786 time to fit residues: 97.1030 Evaluate side-chains 129 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 62 time to evaluate : 3.223 ------------------------------------------------------------------------------- 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 555 SER 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 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 501 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS 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 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 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN 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 105 ILE 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 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 367 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 709 ASN 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 1043 CYS 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 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 61 ARG 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 204 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 330 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 42 GLN D 86 ASN ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.087790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.060466 restraints weight = 226694.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.059712 restraints weight = 219031.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.060020 restraints weight = 206029.574| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 30876 Z= 0.235 Angle : 0.646 11.511 42079 Z= 0.331 Chirality : 0.046 0.372 4762 Planarity : 0.005 0.082 5411 Dihedral : 8.232 100.555 4585 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.71 % Allowed : 15.89 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3819 helix: 1.24 (0.19), residues: 726 sheet: -1.58 (0.18), residues: 743 loop : -1.26 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 633 HIS 0.005 0.001 HIS A1058 PHE 0.021 0.002 PHE A 559 TYR 0.032 0.002 TYR B 170 ARG 0.008 0.001 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 18) link_NAG-ASN : angle 3.33026 ( 54) hydrogen bonds : bond 0.04836 ( 1083) hydrogen bonds : angle 6.55048 ( 2907) SS BOND : bond 0.00385 ( 46) SS BOND : angle 1.23678 ( 92) covalent geometry : bond 0.00509 (30812) covalent geometry : angle 0.63324 (41933) *********************** 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 156 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 66 time to evaluate : 3.518 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: 0.0352 (OUTLIER) cc_final: 0.0011 (tp) REVERT: A 855 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7271 (m-10) REVERT: B 172 SER cc_start: -0.1321 (OUTLIER) cc_final: -0.1637 (t) REVERT: B 204 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.3687 (m-80) REVERT: B 277 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4880 (mm) REVERT: B 573 THR cc_start: -0.0591 (OUTLIER) cc_final: -0.2160 (t) REVERT: B 727 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8462 (mm) REVERT: B 900 MET cc_start: 0.7854 (mtp) cc_final: 0.7485 (mtp) REVERT: C 18 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 167 THR cc_start: -0.1005 (OUTLIER) cc_final: -0.2123 (t) REVERT: C 196 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.4844 (p0) REVERT: C 218 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6481 (mt0) REVERT: C 258 TRP cc_start: 0.2274 (OUTLIER) cc_final: 0.0932 (p90) REVERT: C 902 MET cc_start: 0.7850 (tpt) cc_final: 0.7564 (tpp) REVERT: C 1050 MET cc_start: 0.6665 (ptp) cc_final: 0.6342 (ptp) REVERT: D 37 MET cc_start: -0.0399 (mmt) cc_final: -0.0957 (mtm) REVERT: E 4 MET cc_start: 0.8437 (pmm) cc_final: 0.7630 (pmm) REVERT: G 90 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.6835 (p-80) outliers start: 90 outliers final: 64 residues processed: 153 average time/residue: 0.4249 time to fit residues: 113.2665 Evaluate side-chains 141 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 64 time to evaluate : 3.812 ------------------------------------------------------------------------------- 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 440 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 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 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 277 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 524 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 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 18 LEU 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 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 602 THR Chi-restraints excluded: chain C residue 677 GLN 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 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 8 VAL Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 61 ARG 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 60 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 258 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 52 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.088310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.060870 restraints weight = 226230.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.060524 restraints weight = 213566.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.060469 restraints weight = 198018.337| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30876 Z= 0.138 Angle : 0.591 12.121 42079 Z= 0.298 Chirality : 0.045 0.369 4762 Planarity : 0.004 0.080 5411 Dihedral : 8.016 101.600 4585 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3819 helix: 1.35 (0.19), residues: 726 sheet: -1.49 (0.18), residues: 737 loop : -1.20 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C1048 PHE 0.021 0.001 PHE B 168 TYR 0.017 0.001 TYR B 170 ARG 0.016 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 18) link_NAG-ASN : angle 2.99935 ( 54) hydrogen bonds : bond 0.04256 ( 1083) hydrogen bonds : angle 6.37379 ( 2907) SS BOND : bond 0.00301 ( 46) SS BOND : angle 1.13466 ( 92) covalent geometry : bond 0.00295 (30812) covalent geometry : angle 0.57942 (41933) *********************** 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 149 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 63 time to evaluate : 3.131 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: A 110 LEU cc_start: 0.0692 (OUTLIER) cc_final: 0.0388 (tp) REVERT: A 855 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: B 204 TYR cc_start: 0.5095 (OUTLIER) cc_final: 0.3148 (m-80) REVERT: B 573 THR cc_start: -0.1151 (OUTLIER) cc_final: -0.2670 (t) REVERT: B 727 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8437 (mm) REVERT: C 18 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7719 (tp) REVERT: C 167 THR cc_start: -0.1631 (OUTLIER) cc_final: -0.2636 (t) REVERT: C 196 ASN cc_start: 0.5497 (OUTLIER) cc_final: 0.5046 (p0) REVERT: C 218 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6467 (mt0) REVERT: C 258 TRP cc_start: 0.2059 (OUTLIER) cc_final: 0.0881 (p90) REVERT: C 902 MET cc_start: 0.7849 (tpt) cc_final: 0.7587 (tpp) REVERT: D 37 MET cc_start: -0.0031 (mmt) cc_final: -0.0639 (mtm) REVERT: E 4 MET cc_start: 0.8549 (pmm) cc_final: 0.7915 (pmm) outliers start: 86 outliers final: 63 residues processed: 147 average time/residue: 0.4139 time to fit residues: 105.1847 Evaluate side-chains 135 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 62 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 294 ASP 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 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 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 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 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 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN 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 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 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 677 GLN 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 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 90 HIS 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 32 TRP Chi-restraints excluded: chain G residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 154 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 325 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 362 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** 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 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.093708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.083171 restraints weight = 279775.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.084308 restraints weight = 203268.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.084598 restraints weight = 160921.367| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 30876 Z= 0.240 Angle : 0.669 12.746 42079 Z= 0.345 Chirality : 0.047 0.362 4762 Planarity : 0.005 0.084 5411 Dihedral : 8.325 104.022 4584 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.29 % Allowed : 16.28 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3819 helix: 1.09 (0.19), residues: 729 sheet: -1.71 (0.17), residues: 761 loop : -1.32 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 39 HIS 0.008 0.001 HIS G 90 PHE 0.024 0.002 PHE A 559 TYR 0.037 0.002 TYR B 170 ARG 0.012 0.001 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 18) link_NAG-ASN : angle 3.10561 ( 54) hydrogen bonds : bond 0.04938 ( 1083) hydrogen bonds : angle 6.71372 ( 2907) SS BOND : bond 0.00505 ( 46) SS BOND : angle 1.49261 ( 92) covalent geometry : bond 0.00521 (30812) covalent geometry : angle 0.65709 (41933) ********************** 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 142 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 66 time to evaluate : 3.552 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: -0.0227 (OUTLIER) cc_final: -0.0563 (tp) REVERT: A 855 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: B 172 SER cc_start: 0.0698 (OUTLIER) cc_final: 0.0001 (t) REVERT: B 204 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.4382 (m-80) REVERT: B 573 THR cc_start: 0.0214 (OUTLIER) cc_final: -0.1671 (t) REVERT: B 727 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 1126 CYS cc_start: 0.4430 (m) cc_final: 0.3946 (m) REVERT: C 167 THR cc_start: -0.1310 (OUTLIER) cc_final: -0.2486 (t) REVERT: C 196 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4571 (p0) REVERT: C 218 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6287 (mt0) REVERT: C 258 TRP cc_start: 0.4458 (OUTLIER) cc_final: 0.1460 (p90) REVERT: C 902 MET cc_start: 0.7790 (tpt) cc_final: 0.7505 (tpp) REVERT: D 37 MET cc_start: -0.0077 (mmt) cc_final: -0.0372 (mtt) REVERT: E 4 MET cc_start: 0.6871 (pmm) cc_final: 0.5935 (pmm) outliers start: 76 outliers final: 63 residues processed: 139 average time/residue: 0.3718 time to fit residues: 90.0658 Evaluate side-chains 137 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 64 time to evaluate : 3.143 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 238 PHE 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 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 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 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 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 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 677 GLN 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 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 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL 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 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 42 optimal weight: 0.0970 chunk 323 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 283 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** B 52 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.087873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.061044 restraints weight = 227696.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.060645 restraints weight = 209409.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.060794 restraints weight = 192330.391| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30876 Z= 0.128 Angle : 0.592 12.135 42079 Z= 0.298 Chirality : 0.045 0.363 4762 Planarity : 0.004 0.065 5411 Dihedral : 7.971 104.613 4583 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.14 % Allowed : 16.49 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3819 helix: 1.32 (0.19), residues: 729 sheet: -1.57 (0.18), residues: 731 loop : -1.24 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS C1048 PHE 0.021 0.001 PHE B 168 TYR 0.022 0.001 TYR A 873 ARG 0.007 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 18) link_NAG-ASN : angle 2.85558 ( 54) hydrogen bonds : bond 0.04215 ( 1083) hydrogen bonds : angle 6.42460 ( 2907) SS BOND : bond 0.00300 ( 46) SS BOND : angle 1.20825 ( 92) covalent geometry : bond 0.00275 (30812) covalent geometry : angle 0.58132 (41933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13536.47 seconds wall clock time: 242 minutes 42.62 seconds (14562.62 seconds total)