Starting phenix.real_space_refine on Wed May 28 03:00:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbf_38216/05_2025/8xbf_38216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbf_38216/05_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_38216/05_2025/8xbf_38216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbf_38216/05_2025/8xbf_38216.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbf_38216/05_2025/8xbf_38216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbf_38216/05_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): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 17.65, per 1000 atoms: 0.59 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: 7.42 Conformation dependent library (CDL) restraints added in 3.8 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: 4.20 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: 14.01 Time building geometry restraints manager: 8.68 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: 0.09 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 68.330 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.150 ------------------------------------------------------------------------------- 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 : 3.301 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: 0.3765 time to fit residues: 158.0814 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 : 3.122 ------------------------------------------------------------------------------- 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 = 225311.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.061380 restraints weight = 206484.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.061116 restraints weight = 206086.713| |-----------------------------------------------------------------------------| 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 : 3.186 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: -0.1536 (mptt) REVERT: A 740 MET cc_start: 0.8948 (tpt) cc_final: 0.8650 (tpt) REVERT: A 855 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: A 873 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.6110 (t80) REVERT: B 204 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.3301 (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: 0.4930 (OUTLIER) cc_final: 0.4475 (p0) REVERT: C 258 TRP cc_start: 0.1950 (OUTLIER) cc_final: 0.0691 (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: 0.7689 (pmm) cc_final: 0.6829 (pmm) outliers start: 141 outliers final: 77 residues processed: 206 average time/residue: 0.4017 time to fit residues: 138.1624 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 : 3.266 ------------------------------------------------------------------------------- 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: 0.8980 chunk 96 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.088901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.060607 restraints weight = 225522.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.060508 restraints weight = 206947.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.060263 restraints weight = 198643.211| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 30876 Z= 0.226 Angle : 0.655 11.424 42079 Z= 0.337 Chirality : 0.047 0.434 4762 Planarity : 0.005 0.069 5411 Dihedral : 9.243 106.318 4637 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.98 % Allowed : 13.51 % Favored : 82.51 % 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: -1.45 (0.13), residues: 3819 helix: 0.94 (0.19), residues: 744 sheet: -1.55 (0.18), residues: 731 loop : -1.44 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 436 HIS 0.005 0.001 HIS A1058 PHE 0.028 0.002 PHE A 559 TYR 0.029 0.002 TYR B 170 ARG 0.009 0.001 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 18) link_NAG-ASN : angle 3.42261 ( 54) hydrogen bonds : bond 0.05077 ( 1083) hydrogen bonds : angle 6.96505 ( 2907) SS BOND : bond 0.00462 ( 46) SS BOND : angle 1.19893 ( 92) covalent geometry : bond 0.00487 (30812) covalent geometry : angle 0.64227 (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 201 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 69 time to evaluate : 3.260 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: 0.7293 (m-80) REVERT: B 172 SER cc_start: -0.1973 (OUTLIER) cc_final: -0.2321 (t) REVERT: B 204 TYR cc_start: 0.5548 (OUTLIER) cc_final: 0.3448 (m-80) REVERT: B 573 THR cc_start: -0.0522 (OUTLIER) cc_final: -0.2096 (t) REVERT: B 727 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8352 (mm) REVERT: C 18 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 196 ASN cc_start: 0.5164 (OUTLIER) cc_final: 0.4659 (p0) REVERT: C 258 TRP cc_start: 0.1950 (OUTLIER) cc_final: 0.0830 (p90) REVERT: C 284 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6543 (m) REVERT: C 693 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4775 (pp) REVERT: C 1073 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7110 (tmtt) REVERT: D 37 MET cc_start: -0.1752 (OUTLIER) cc_final: -0.2200 (mtt) REVERT: E 4 MET cc_start: 0.8084 (pmm) cc_final: 0.7204 (pmm) REVERT: F 37 MET cc_start: 0.7778 (mpp) cc_final: 0.7424 (mpp) REVERT: G 90 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7100 (m-70) outliers start: 132 outliers final: 78 residues processed: 195 average time/residue: 0.3908 time to fit residues: 128.5779 Evaluate side-chains 155 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 64 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 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 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: 0.0470 chunk 77 optimal weight: 3.9990 chunk 259 optimal weight: 0.0970 chunk 335 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 357 optimal weight: 0.2980 overall best weight: 0.8878 ------------------------------------------------------------------------------- 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 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 218 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.089771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.062039 restraints weight = 227051.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.061544 restraints weight = 208414.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.061545 restraints weight = 198190.662| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30876 Z= 0.121 Angle : 0.577 11.053 42079 Z= 0.291 Chirality : 0.045 0.422 4762 Planarity : 0.004 0.058 5411 Dihedral : 8.589 99.496 4623 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.44 % Allowed : 13.78 % Favored : 82.79 % 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: -1.22 (0.13), residues: 3819 helix: 1.16 (0.19), residues: 747 sheet: -1.44 (0.18), residues: 708 loop : -1.30 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS A1083 PHE 0.017 0.001 PHE A 559 TYR 0.019 0.001 TYR A 873 ARG 0.004 0.000 ARG E 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 18) link_NAG-ASN : angle 3.06618 ( 54) hydrogen bonds : bond 0.04281 ( 1083) hydrogen bonds : angle 6.52031 ( 2907) SS BOND : bond 0.00279 ( 46) SS BOND : angle 1.08362 ( 92) covalent geometry : bond 0.00252 (30812) covalent geometry : angle 0.56499 (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 183 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 69 time to evaluate : 3.250 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: 0.8091 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: B 204 TYR cc_start: 0.4756 (OUTLIER) cc_final: 0.2998 (m-80) REVERT: B 573 THR cc_start: -0.1484 (OUTLIER) cc_final: -0.2817 (t) REVERT: B 727 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 900 MET cc_start: 0.7783 (mtp) cc_final: 0.7475 (mtp) REVERT: C 18 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7871 (tp) REVERT: C 23 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: C 196 ASN cc_start: 0.5172 (OUTLIER) cc_final: 0.4696 (p0) REVERT: C 242 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7549 (tt) REVERT: C 258 TRP cc_start: 0.2087 (OUTLIER) cc_final: 0.0965 (p90) REVERT: C 693 ILE cc_start: 0.5066 (OUTLIER) cc_final: 0.4823 (pp) REVERT: D 37 MET cc_start: -0.1638 (OUTLIER) cc_final: -0.2040 (mtp) REVERT: E 4 MET cc_start: 0.7963 (pmm) cc_final: 0.7048 (pmm) REVERT: G 90 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7192 (m90) outliers start: 114 outliers final: 66 residues processed: 178 average time/residue: 0.3769 time to fit residues: 113.5408 Evaluate side-chains 140 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 62 time to evaluate : 3.449 ------------------------------------------------------------------------------- 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 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 1106 GLN 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 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 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 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 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 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 37 MET 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: 0.4980 chunk 201 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 355 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.089613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.061863 restraints weight = 225095.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.061497 restraints weight = 209555.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.061376 restraints weight = 199936.416| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30876 Z= 0.127 Angle : 0.567 11.998 42079 Z= 0.287 Chirality : 0.045 0.411 4762 Planarity : 0.004 0.057 5411 Dihedral : 8.354 98.192 4615 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.20 % Allowed : 14.32 % Favored : 82.48 % 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: -1.15 (0.13), residues: 3819 helix: 1.24 (0.19), residues: 747 sheet: -1.43 (0.18), residues: 724 loop : -1.24 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS B1048 PHE 0.024 0.001 PHE B 43 TYR 0.019 0.001 TYR B 508 ARG 0.006 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 18) link_NAG-ASN : angle 2.94400 ( 54) hydrogen bonds : bond 0.04184 ( 1083) hydrogen bonds : angle 6.38560 ( 2907) SS BOND : bond 0.00276 ( 46) SS BOND : angle 1.18117 ( 92) covalent geometry : bond 0.00271 (30812) covalent geometry : angle 0.55541 (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 171 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 65 time to evaluate : 3.144 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: 0.0825 (OUTLIER) cc_final: 0.0480 (tp) REVERT: A 855 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: B 204 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.2869 (m-80) REVERT: B 573 THR cc_start: -0.1325 (OUTLIER) cc_final: -0.2716 (t) REVERT: B 727 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 900 MET cc_start: 0.7596 (mtp) cc_final: 0.7274 (mtp) REVERT: C 18 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (tp) REVERT: C 196 ASN cc_start: 0.5127 (OUTLIER) cc_final: 0.4603 (p0) REVERT: C 218 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5803 (mt0) REVERT: C 258 TRP cc_start: 0.2024 (OUTLIER) cc_final: 0.0963 (p90) REVERT: C 693 ILE cc_start: 0.5090 (OUTLIER) cc_final: 0.4856 (pp) REVERT: D 37 MET cc_start: -0.0516 (mmt) cc_final: -0.0913 (mtt) REVERT: D 82 PHE cc_start: 0.8777 (m-80) cc_final: 0.8492 (m-80) REVERT: E 4 MET cc_start: 0.8285 (pmm) cc_final: 0.7676 (pmm) REVERT: E 33 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3706 (tp) REVERT: G 50 LYS cc_start: 0.5682 (pttt) cc_final: 0.4692 (ptpp) REVERT: G 90 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7111 (m90) outliers start: 106 outliers final: 68 residues processed: 169 average time/residue: 0.3764 time to fit residues: 107.7147 Evaluate side-chains 139 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 59 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 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 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 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 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 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 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 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 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: 20.0000 chunk 335 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 374 optimal weight: 5.9990 chunk 312 optimal weight: 0.0980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 207 HIS C 901 GLN D 42 GLN D 86 ASN ** F 35 ASN ** 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 = 0.4695 r_free = 0.4695 target = 0.088545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061254 restraints weight = 226163.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060884 restraints weight = 203361.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.062638 restraints weight = 190163.919| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30876 Z= 0.198 Angle : 0.618 11.457 42079 Z= 0.316 Chirality : 0.046 0.395 4762 Planarity : 0.005 0.059 5411 Dihedral : 8.439 99.599 4607 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.32 % Allowed : 15.04 % Favored : 81.64 % 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: -1.29 (0.13), residues: 3819 helix: 1.16 (0.19), residues: 747 sheet: -1.54 (0.18), residues: 754 loop : -1.32 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 32 HIS 0.004 0.001 HIS A1058 PHE 0.029 0.002 PHE B 168 TYR 0.027 0.002 TYR B 170 ARG 0.008 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 18) link_NAG-ASN : angle 2.98616 ( 54) hydrogen bonds : bond 0.04662 ( 1083) hydrogen bonds : angle 6.56991 ( 2907) SS BOND : bond 0.00404 ( 46) SS BOND : angle 1.38682 ( 92) covalent geometry : bond 0.00429 (30812) covalent geometry : angle 0.60624 (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 175 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 65 time to evaluate : 3.330 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: 0.8225 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: B 172 SER cc_start: -0.1834 (OUTLIER) cc_final: -0.2209 (t) REVERT: B 204 TYR cc_start: 0.5151 (OUTLIER) cc_final: 0.3243 (m-80) REVERT: B 371 PHE cc_start: -0.1649 (OUTLIER) cc_final: -0.1879 (t80) REVERT: B 573 THR cc_start: -0.0519 (OUTLIER) cc_final: -0.2265 (t) REVERT: B 727 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 1139 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7573 (p0) REVERT: C 18 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7868 (tp) REVERT: C 167 THR cc_start: -0.1635 (OUTLIER) cc_final: -0.2578 (t) REVERT: C 196 ASN cc_start: 0.5188 (OUTLIER) cc_final: 0.4608 (p0) REVERT: C 218 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6097 (mt0) REVERT: C 258 TRP cc_start: 0.2193 (OUTLIER) cc_final: 0.0928 (p90) REVERT: C 284 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6429 (m) REVERT: C 693 ILE cc_start: 0.5269 (OUTLIER) cc_final: 0.5045 (pp) REVERT: D 22 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.6206 (mmm-85) REVERT: D 37 MET cc_start: -0.0601 (mmt) cc_final: -0.0936 (mtt) REVERT: E 4 MET cc_start: 0.8037 (pmm) cc_final: 0.7323 (pmm) REVERT: G 70 GLU cc_start: 0.3844 (OUTLIER) cc_final: 0.3578 (tt0) REVERT: G 90 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.6790 (m90) outliers start: 110 outliers final: 71 residues processed: 174 average time/residue: 0.3777 time to fit residues: 112.1183 Evaluate side-chains 150 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 63 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 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 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 266 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 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 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 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 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 70 GLU 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: 9.9990 chunk 138 optimal weight: 0.7980 chunk 374 optimal weight: 0.2980 chunk 210 optimal weight: 8.9990 chunk 258 optimal weight: 50.0000 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 312 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 437 ASN ** 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** 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 = 0.4714 r_free = 0.4714 target = 0.088880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.061376 restraints weight = 227335.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.060861 restraints weight = 216354.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.060960 restraints weight = 199037.717| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30876 Z= 0.132 Angle : 0.576 11.742 42079 Z= 0.291 Chirality : 0.045 0.387 4762 Planarity : 0.004 0.057 5411 Dihedral : 8.089 97.151 4596 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.92 % Allowed : 15.68 % 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: -1.18 (0.13), residues: 3819 helix: 1.27 (0.19), residues: 747 sheet: -1.49 (0.18), residues: 754 loop : -1.25 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 PHE 0.015 0.001 PHE A 559 TYR 0.024 0.001 TYR B 508 ARG 0.008 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 18) link_NAG-ASN : angle 2.91794 ( 54) hydrogen bonds : bond 0.04223 ( 1083) hydrogen bonds : angle 6.37662 ( 2907) SS BOND : bond 0.00298 ( 46) SS BOND : angle 1.16814 ( 92) covalent geometry : bond 0.00283 (30812) covalent geometry : angle 0.56504 (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 162 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 65 time to evaluate : 3.361 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: 0.0557 (OUTLIER) cc_final: 0.0255 (tp) REVERT: A 855 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: B 204 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.2949 (m-80) REVERT: B 573 THR cc_start: -0.1174 (OUTLIER) cc_final: -0.2801 (t) REVERT: B 727 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8242 (mm) REVERT: C 18 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 167 THR cc_start: -0.1534 (OUTLIER) cc_final: -0.2686 (t) REVERT: C 196 ASN cc_start: 0.5287 (OUTLIER) cc_final: 0.4813 (p0) REVERT: C 218 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: C 258 TRP cc_start: 0.2046 (OUTLIER) cc_final: 0.0936 (p90) REVERT: C 284 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6317 (m) REVERT: C 693 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4858 (pp) REVERT: D 37 MET cc_start: -0.0456 (mmt) cc_final: -0.0843 (mtt) REVERT: E 4 MET cc_start: 0.8410 (pmm) cc_final: 0.7857 (pmm) REVERT: G 90 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.6979 (m90) outliers start: 97 outliers final: 68 residues processed: 161 average time/residue: 0.3882 time to fit residues: 106.1859 Evaluate side-chains 144 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 63 time to evaluate : 3.123 ------------------------------------------------------------------------------- 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 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 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 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 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 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 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: 8.9990 chunk 278 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 330 optimal weight: 0.0670 chunk 181 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 ** 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 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 ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.087793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.060619 restraints weight = 228163.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.060178 restraints weight = 212446.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.060052 restraints weight = 201100.523| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 30876 Z= 0.186 Angle : 0.608 11.365 42079 Z= 0.311 Chirality : 0.045 0.372 4762 Planarity : 0.004 0.059 5411 Dihedral : 8.259 100.883 4595 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.11 % Allowed : 15.59 % Favored : 81.31 % 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: -1.22 (0.13), residues: 3819 helix: 1.28 (0.19), residues: 726 sheet: -1.57 (0.18), residues: 743 loop : -1.25 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.005 0.001 HIS C 207 PHE 0.021 0.001 PHE A 559 TYR 0.026 0.002 TYR B 170 ARG 0.008 0.000 ARG F 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 18) link_NAG-ASN : angle 2.92641 ( 54) hydrogen bonds : bond 0.04559 ( 1083) hydrogen bonds : angle 6.48781 ( 2907) SS BOND : bond 0.00350 ( 46) SS BOND : angle 1.23161 ( 92) covalent geometry : bond 0.00403 (30812) covalent geometry : angle 0.59688 (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 169 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 66 time to evaluate : 3.413 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: 0.0623 (OUTLIER) cc_final: 0.0303 (tp) REVERT: A 282 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7440 (m110) REVERT: A 855 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: B 172 SER cc_start: -0.1557 (OUTLIER) cc_final: -0.1848 (t) REVERT: B 204 TYR cc_start: 0.5302 (OUTLIER) cc_final: 0.3200 (m-80) REVERT: B 573 THR cc_start: -0.0955 (OUTLIER) cc_final: -0.2434 (t) REVERT: B 727 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8462 (mm) REVERT: B 900 MET cc_start: 0.7665 (mtp) cc_final: 0.7133 (mtm) REVERT: C 18 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (tp) REVERT: C 167 THR cc_start: -0.1323 (OUTLIER) cc_final: -0.2350 (t) REVERT: C 196 ASN cc_start: 0.5414 (OUTLIER) cc_final: 0.4899 (p0) REVERT: C 218 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: C 258 TRP cc_start: 0.2096 (OUTLIER) cc_final: 0.0898 (p90) REVERT: C 693 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4866 (pp) REVERT: D 37 MET cc_start: -0.0315 (mmt) cc_final: -0.0706 (mtt) REVERT: E 4 MET cc_start: 0.8544 (pmm) cc_final: 0.7918 (pmm) REVERT: G 90 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.6759 (p-80) outliers start: 103 outliers final: 72 residues processed: 166 average time/residue: 0.3891 time to fit residues: 109.1955 Evaluate side-chains 150 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 64 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 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 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 691 SER 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 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 677 GLN 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 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 31 SER 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: 2.9990 chunk 21 optimal weight: 7.9990 chunk 178 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.087623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.060785 restraints weight = 227353.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.060323 restraints weight = 210543.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.060180 restraints weight = 205722.727| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30876 Z= 0.175 Angle : 0.606 11.402 42079 Z= 0.308 Chirality : 0.045 0.367 4762 Planarity : 0.004 0.060 5411 Dihedral : 8.199 102.366 4593 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.71 % Allowed : 16.04 % Favored : 81.25 % 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: 1.28 (0.19), residues: 726 sheet: -1.57 (0.18), residues: 713 loop : -1.23 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS C 207 PHE 0.016 0.001 PHE A 559 TYR 0.023 0.001 TYR B 170 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 18) link_NAG-ASN : angle 2.89980 ( 54) hydrogen bonds : bond 0.04484 ( 1083) hydrogen bonds : angle 6.48089 ( 2907) SS BOND : bond 0.00340 ( 46) SS BOND : angle 1.18092 ( 92) covalent geometry : bond 0.00377 (30812) covalent geometry : angle 0.59519 (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 156 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 66 time to evaluate : 3.244 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: 0.0595 (OUTLIER) cc_final: 0.0276 (tp) REVERT: A 282 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (m110) REVERT: A 855 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: B 172 SER cc_start: -0.1551 (OUTLIER) cc_final: -0.1829 (t) REVERT: B 204 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.3254 (m-80) REVERT: B 573 THR cc_start: -0.1010 (OUTLIER) cc_final: -0.2516 (t) REVERT: B 727 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 18 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7778 (tp) REVERT: C 167 THR cc_start: -0.1505 (OUTLIER) cc_final: -0.2534 (t) REVERT: C 196 ASN cc_start: 0.5708 (OUTLIER) cc_final: 0.5250 (p0) REVERT: C 218 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6574 (mt0) REVERT: C 258 TRP cc_start: 0.2127 (OUTLIER) cc_final: 0.0907 (p90) REVERT: C 559 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.4967 (t80) REVERT: C 693 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4899 (pp) REVERT: D 37 MET cc_start: 0.0178 (mmt) cc_final: -0.0230 (mtt) REVERT: E 4 MET cc_start: 0.8485 (pmm) cc_final: 0.7849 (pmm) REVERT: E 71 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: G 90 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.6596 (p-80) outliers start: 90 outliers final: 69 residues processed: 154 average time/residue: 0.3841 time to fit residues: 101.8112 Evaluate side-chains 149 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 64 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 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 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 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 691 SER 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 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE 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 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 53 ILE Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 154 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 364 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** 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** C 901 GLN ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.087262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.060383 restraints weight = 228253.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.060374 restraints weight = 200204.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.060257 restraints weight = 193193.448| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2955 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= 0.179 Angle : 0.610 11.456 42079 Z= 0.312 Chirality : 0.045 0.365 4762 Planarity : 0.005 0.064 5411 Dihedral : 8.224 104.350 4593 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.80 % Allowed : 16.04 % Favored : 81.16 % 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: -1.23 (0.13), residues: 3819 helix: 1.25 (0.19), residues: 729 sheet: -1.58 (0.18), residues: 737 loop : -1.25 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 PHE 0.028 0.001 PHE A 347 TYR 0.040 0.002 TYR A 873 ARG 0.011 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 18) link_NAG-ASN : angle 2.88462 ( 54) hydrogen bonds : bond 0.04544 ( 1083) hydrogen bonds : angle 6.53413 ( 2907) SS BOND : bond 0.00404 ( 46) SS BOND : angle 1.17378 ( 92) covalent geometry : bond 0.00388 (30812) covalent geometry : angle 0.59978 (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 159 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 66 time to evaluate : 3.408 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: 0.0791 (OUTLIER) cc_final: 0.0482 (tp) REVERT: A 282 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7493 (m110) REVERT: A 855 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: B 172 SER cc_start: -0.1582 (OUTLIER) cc_final: -0.1868 (t) REVERT: B 204 TYR cc_start: 0.5403 (OUTLIER) cc_final: 0.3340 (m-80) REVERT: B 573 THR cc_start: -0.0786 (OUTLIER) cc_final: -0.2242 (t) REVERT: B 727 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 18 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7761 (tp) REVERT: C 167 THR cc_start: -0.1653 (OUTLIER) cc_final: -0.2673 (t) REVERT: C 196 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5600 (p0) REVERT: C 218 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6668 (mt0) REVERT: C 258 TRP cc_start: 0.2205 (OUTLIER) cc_final: 0.0914 (p90) REVERT: C 559 PHE cc_start: 0.5402 (OUTLIER) cc_final: 0.4916 (t80) REVERT: C 693 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4912 (pp) REVERT: D 37 MET cc_start: 0.0240 (mmt) cc_final: -0.0187 (mtt) REVERT: E 4 MET cc_start: 0.8555 (pmm) cc_final: 0.7956 (pmm) REVERT: E 71 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6079 (m-80) REVERT: G 90 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.6578 (p-80) outliers start: 93 outliers final: 73 residues processed: 156 average time/residue: 0.3868 time to fit residues: 103.4358 Evaluate side-chains 153 residues out of total 3317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 64 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 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 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 691 SER 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 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE 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 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 53 ILE Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain E residue 71 PHE 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 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 42 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** 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** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.087724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.061168 restraints weight = 227745.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.060930 restraints weight = 203487.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.060615 restraints weight = 198260.823| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30876 Z= 0.138 Angle : 0.582 11.743 42079 Z= 0.294 Chirality : 0.045 0.361 4762 Planarity : 0.004 0.059 5411 Dihedral : 8.005 105.358 4592 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.65 % Allowed : 16.13 % Favored : 81.22 % 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: -1.10 (0.13), residues: 3819 helix: 1.35 (0.19), residues: 729 sheet: -1.50 (0.18), residues: 707 loop : -1.17 (0.13), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 PHE 0.019 0.001 PHE A 347 TYR 0.024 0.001 TYR A 873 ARG 0.008 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 18) link_NAG-ASN : angle 2.76929 ( 54) hydrogen bonds : bond 0.04215 ( 1083) hydrogen bonds : angle 6.36156 ( 2907) SS BOND : bond 0.00323 ( 46) SS BOND : angle 1.20768 ( 92) covalent geometry : bond 0.00296 (30812) covalent geometry : angle 0.57143 (41933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12614.34 seconds wall clock time: 220 minutes 32.96 seconds (13232.96 seconds total)