Starting phenix.real_space_refine on Sat Jun 21 07:12:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmg_38476/06_2025/8xmg_38476.cif" } resolution = 2.9 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= 0.001 sd= 0.020 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 107 5.16 5 C 15602 2.51 5 N 4043 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24476 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 55, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7942 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 55, 'TRANS': 960} Chain breaks: 7 Chain: "C" Number of atoms: 8002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8002 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 55, 'TRANS': 967} Chain breaks: 7 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.57, per 1000 atoms: 0.64 Number of scatterers: 24476 At special positions: 0 Unit cell: (135.744, 135.744, 164.832, 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 107 16.00 O 4724 8.00 N 4043 7.00 C 15602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " 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 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 61 " " NAG B1314 " - " ASN B1098 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 61 " Time building additional restraints: 5.58 Conformation dependent library (CDL) restraints added in 3.2 seconds 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 42 sheets defined 25.1% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.741A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.366A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' 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 removed outlier: 3.506A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.000A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.072A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.746A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.520A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.504A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.584A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.268A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.170A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.236A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.840A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.507A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.738A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.559A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.503A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.521A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.885A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (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 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.747A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.998A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.740A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.813A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 3.641A pdb=" N THR A 23 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.501A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.322A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.083A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.898A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.906A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.517A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.603A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.731A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 23 through 30 removed outlier: 7.708A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.624A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.875A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.931A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.615A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.379A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.494A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD5, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.832A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.067A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.815A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1121 1044 hydrogen bonds defined for protein. 2895 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: 11.29 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7282 1.33 - 1.46: 6302 1.46 - 1.59: 11316 1.59 - 1.71: 1 1.71 - 1.84: 133 Bond restraints: 25034 Sorted by residual: bond pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.40e+00 bond pdb=" N ASN A1135 " pdb=" CA ASN A1135 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 bond pdb=" N SER C1097 " pdb=" CA SER C1097 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.02e+00 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.26e-02 6.30e+03 6.73e+00 bond pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.22e-02 6.72e+03 6.68e+00 ... (remaining 25029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 32969 1.55 - 3.11: 945 3.11 - 4.66: 134 4.66 - 6.21: 16 6.21 - 7.77: 4 Bond angle restraints: 34068 Sorted by residual: angle pdb=" C PRO B 527 " pdb=" CA PRO B 527 " pdb=" CB PRO B 527 " ideal model delta sigma weight residual 111.64 105.55 6.09 1.26e+00 6.30e-01 2.34e+01 angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 121.02 113.92 7.10 1.48e+00 4.57e-01 2.30e+01 angle pdb=" C PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta sigma weight residual 111.56 104.88 6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 122.09 128.00 -5.91 1.48e+00 4.57e-01 1.59e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.48 3.14 7.90e-01 1.60e+00 1.58e+01 ... (remaining 34063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14159 17.97 - 35.93: 1037 35.93 - 53.90: 180 53.90 - 71.86: 50 71.86 - 89.83: 19 Dihedral angle restraints: 15445 sinusoidal: 6517 harmonic: 8928 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -3.20 -82.80 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 14.12 78.88 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -9.03 -76.97 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 15442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 3977 0.331 - 0.661: 4 0.661 - 0.992: 1 0.992 - 1.323: 1 1.323 - 1.654: 1 Chirality restraints: 3984 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3981 not shown) Planarity restraints: 4394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.322 2.00e-02 2.50e+03 2.80e-01 9.80e+02 pdb=" C7 NAG C1311 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.495 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1313 " -0.249 2.00e-02 2.50e+03 2.13e-01 5.69e+02 pdb=" C7 NAG B1313 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1313 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B1313 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG B1313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.243 2.00e-02 2.50e+03 2.08e-01 5.41e+02 pdb=" C7 NAG B1305 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.182 2.00e-02 2.50e+03 ... (remaining 4391 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3011 2.75 - 3.29: 23349 3.29 - 3.83: 39892 3.83 - 4.36: 46428 4.36 - 4.90: 81760 Nonbonded interactions: 194440 Sorted by model distance: nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.216 3.040 nonbonded pdb=" OG SER C 112 " pdb=" OE1 GLN C 134 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 94 " pdb=" OE1 GLU B 96 " model vdw 2.237 3.040 nonbonded pdb=" O GLN C 580 " pdb=" O6 NAG C1303 " model vdw 2.246 3.040 ... (remaining 194435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 143 or resid 159 through 176 or resid 187 throu \ gh 676 or resid 689 through 826 or resid 855 through 1139 or resid 1301 through \ 1312)) selection = (chain 'B' and (resid 20 through 826 or resid 855 through 1139 or resid 1301 thr \ ough 1312)) selection = (chain 'C' and (resid 20 through 143 or resid 159 through 176 or resid 187 throu \ gh 676 or resid 689 through 826 or resid 855 through 1139 or resid 1301 through \ 1312)) } 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 individual isotropic 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: 16.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.130 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.050 25108 Z= 0.212 Angle : 0.655 15.311 34254 Z= 0.351 Chirality : 0.059 1.654 3984 Planarity : 0.009 0.280 4356 Dihedral : 12.814 89.830 9585 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3014 helix: 2.20 (0.21), residues: 641 sheet: 0.56 (0.18), residues: 710 loop : -0.88 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS B1058 PHE 0.026 0.001 PHE C 823 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 38) link_NAG-ASN : angle 3.84720 ( 114) hydrogen bonds : bond 0.12867 ( 1020) hydrogen bonds : angle 6.62761 ( 2895) SS BOND : bond 0.00565 ( 36) SS BOND : angle 1.49962 ( 72) covalent geometry : bond 0.00412 (25034) covalent geometry : angle 0.61385 (34068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 771 time to evaluate : 2.380 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7399 (pt0) cc_final: 0.7178 (pt0) REVERT: A 32 PHE cc_start: 0.8735 (m-80) cc_final: 0.8451 (m-80) REVERT: A 43 PHE cc_start: 0.8810 (t80) cc_final: 0.8504 (t80) REVERT: A 130 VAL cc_start: 0.7535 (t) cc_final: 0.7234 (p) REVERT: A 305 SER cc_start: 0.8462 (t) cc_final: 0.8204 (p) REVERT: A 306 PHE cc_start: 0.8803 (m-80) cc_final: 0.8427 (m-80) REVERT: A 391 CYS cc_start: 0.7070 (m) cc_final: 0.6677 (m) REVERT: A 422 ASN cc_start: 0.6442 (m110) cc_final: 0.6206 (m110) REVERT: A 505 HIS cc_start: 0.7230 (m-70) cc_final: 0.6761 (m-70) REVERT: A 574 ASP cc_start: 0.7700 (t70) cc_final: 0.7430 (t0) REVERT: A 576 VAL cc_start: 0.9127 (t) cc_final: 0.8896 (p) REVERT: A 581 THR cc_start: 0.7876 (m) cc_final: 0.7571 (p) REVERT: A 660 TYR cc_start: 0.8398 (m-80) cc_final: 0.8160 (m-80) REVERT: A 723 THR cc_start: 0.8467 (p) cc_final: 0.8250 (m) REVERT: A 725 GLU cc_start: 0.7905 (tt0) cc_final: 0.7621 (tt0) REVERT: A 814 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8205 (mmtt) REVERT: A 950 ASP cc_start: 0.7244 (m-30) cc_final: 0.6684 (m-30) REVERT: A 1038 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8084 (mmtm) REVERT: A 1045 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7431 (mmtm) REVERT: A 1096 VAL cc_start: 0.8428 (t) cc_final: 0.8198 (m) REVERT: B 53 ASP cc_start: 0.7294 (t0) cc_final: 0.7072 (t0) REVERT: B 127 VAL cc_start: 0.8305 (t) cc_final: 0.7983 (m) REVERT: B 221 SER cc_start: 0.8471 (m) cc_final: 0.8270 (m) REVERT: B 309 GLU cc_start: 0.7602 (mp0) cc_final: 0.7285 (mp0) REVERT: B 328 ARG cc_start: 0.7461 (mmm160) cc_final: 0.7236 (mtp180) REVERT: B 436 TRP cc_start: 0.6457 (p90) cc_final: 0.6192 (p90) REVERT: B 557 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8152 (mttp) REVERT: B 574 ASP cc_start: 0.7346 (t70) cc_final: 0.7026 (t0) REVERT: B 619 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 658 ASN cc_start: 0.7705 (p0) cc_final: 0.7490 (p0) REVERT: B 723 THR cc_start: 0.8431 (p) cc_final: 0.8090 (t) REVERT: B 731 MET cc_start: 0.8923 (ptt) cc_final: 0.8699 (ptm) REVERT: B 735 SER cc_start: 0.8551 (m) cc_final: 0.8324 (t) REVERT: B 736 VAL cc_start: 0.8886 (m) cc_final: 0.8602 (t) REVERT: B 776 LYS cc_start: 0.8361 (tttm) cc_final: 0.7980 (tttm) REVERT: B 780 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 790 LYS cc_start: 0.7962 (mppt) cc_final: 0.7713 (mppt) REVERT: B 823 PHE cc_start: 0.7185 (m-80) cc_final: 0.6952 (m-80) REVERT: B 867 ASP cc_start: 0.7760 (m-30) cc_final: 0.7559 (m-30) REVERT: B 868 GLU cc_start: 0.7674 (mp0) cc_final: 0.7388 (mp0) REVERT: B 952 VAL cc_start: 0.8587 (t) cc_final: 0.8383 (m) REVERT: B 979 ASP cc_start: 0.7756 (t70) cc_final: 0.7445 (t70) REVERT: B 1002 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7861 (tp-100) REVERT: B 1038 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7947 (mmtm) REVERT: B 1096 VAL cc_start: 0.8571 (t) cc_final: 0.8241 (m) REVERT: B 1107 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7512 (mmt90) REVERT: C 24 ARG cc_start: 0.5154 (mtm-85) cc_final: 0.3953 (ttp80) REVERT: C 100 ILE cc_start: 0.8426 (tp) cc_final: 0.8187 (pp) REVERT: C 155 SER cc_start: 0.8692 (m) cc_final: 0.8273 (t) REVERT: C 156 GLU cc_start: 0.7180 (pm20) cc_final: 0.6787 (pp20) REVERT: C 224 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7710 (mt-10) REVERT: C 305 SER cc_start: 0.8655 (t) cc_final: 0.8330 (p) REVERT: C 308 VAL cc_start: 0.8665 (t) cc_final: 0.8461 (p) REVERT: C 515 PHE cc_start: 0.6823 (m-80) cc_final: 0.6338 (m-80) REVERT: C 555 SER cc_start: 0.8591 (t) cc_final: 0.7236 (p) REVERT: C 556 ASN cc_start: 0.8040 (m110) cc_final: 0.7757 (p0) REVERT: C 576 VAL cc_start: 0.8979 (t) cc_final: 0.8577 (p) REVERT: C 578 ASP cc_start: 0.7880 (t0) cc_final: 0.7486 (t70) REVERT: C 581 THR cc_start: 0.7955 (m) cc_final: 0.7178 (t) REVERT: C 584 ILE cc_start: 0.8240 (mm) cc_final: 0.7789 (mm) REVERT: C 651 ILE cc_start: 0.8590 (pt) cc_final: 0.8312 (mt) REVERT: C 661 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6717 (tm-30) REVERT: C 790 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7822 (mtmm) REVERT: C 805 ILE cc_start: 0.8281 (mm) cc_final: 0.8069 (pt) REVERT: C 811 LYS cc_start: 0.8130 (tttm) cc_final: 0.7666 (tttm) REVERT: C 990 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6901 (mm-30) REVERT: C 1041 ASP cc_start: 0.7756 (m-30) cc_final: 0.7410 (m-30) REVERT: C 1073 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7844 (mmmm) outliers start: 3 outliers final: 5 residues processed: 773 average time/residue: 1.3811 time to fit residues: 1243.2296 Evaluate side-chains 612 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 607 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 207 HIS A 354 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 710 ASN A 751 ASN A 784 GLN A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 613 GLN B 710 ASN B 935 GLN B 957 GLN B1010 GLN C 26 GLN C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN C 960 ASN C 978 ASN C1088 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129367 restraints weight = 35761.948| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.42 r_work: 0.3514 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25108 Z= 0.206 Angle : 0.638 12.512 34254 Z= 0.324 Chirality : 0.049 0.450 3984 Planarity : 0.004 0.056 4356 Dihedral : 6.393 101.722 4088 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.06 % Allowed : 12.05 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3014 helix: 2.37 (0.20), residues: 634 sheet: 0.60 (0.18), residues: 696 loop : -0.87 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 353 HIS 0.009 0.001 HIS A 207 PHE 0.023 0.002 PHE A 140 TYR 0.022 0.002 TYR B 279 ARG 0.007 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 38) link_NAG-ASN : angle 3.13251 ( 114) hydrogen bonds : bond 0.05019 ( 1020) hydrogen bonds : angle 5.67574 ( 2895) SS BOND : bond 0.00450 ( 36) SS BOND : angle 2.13672 ( 72) covalent geometry : bond 0.00476 (25034) covalent geometry : angle 0.60531 (34068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 609 time to evaluate : 3.060 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: symmetry clash REVERT: A 26 GLN cc_start: 0.7646 (pt0) cc_final: 0.7393 (pt0) REVERT: A 32 PHE cc_start: 0.8983 (m-80) cc_final: 0.8709 (m-80) REVERT: A 41 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8580 (mttm) REVERT: A 43 PHE cc_start: 0.8774 (t80) cc_final: 0.8544 (t80) REVERT: A 45 SER cc_start: 0.8183 (t) cc_final: 0.7940 (p) REVERT: A 46 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 53 ASP cc_start: 0.7299 (t0) cc_final: 0.7066 (t0) REVERT: A 130 VAL cc_start: 0.7690 (t) cc_final: 0.7486 (p) REVERT: A 205 SER cc_start: 0.8646 (m) cc_final: 0.8401 (p) REVERT: A 305 SER cc_start: 0.8472 (t) cc_final: 0.8198 (p) REVERT: A 409 GLN cc_start: 0.8337 (tt0) cc_final: 0.8134 (tp40) REVERT: A 505 HIS cc_start: 0.7430 (m-70) cc_final: 0.6868 (m-70) REVERT: A 574 ASP cc_start: 0.8058 (t70) cc_final: 0.7669 (t0) REVERT: A 580 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: A 645 THR cc_start: 0.8252 (m) cc_final: 0.7810 (p) REVERT: A 660 TYR cc_start: 0.8577 (m-80) cc_final: 0.8303 (m-80) REVERT: A 714 ILE cc_start: 0.8669 (mm) cc_final: 0.8436 (mp) REVERT: A 723 THR cc_start: 0.8481 (p) cc_final: 0.8278 (m) REVERT: A 725 GLU cc_start: 0.8236 (tt0) cc_final: 0.7955 (tt0) REVERT: A 814 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8218 (mmmm) REVERT: A 933 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8300 (mtpp) REVERT: A 950 ASP cc_start: 0.7454 (m-30) cc_final: 0.6984 (m-30) REVERT: A 968 SER cc_start: 0.8468 (t) cc_final: 0.8266 (m) REVERT: A 1045 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7713 (mmtm) REVERT: A 1096 VAL cc_start: 0.8337 (t) cc_final: 0.8091 (m) REVERT: A 1122 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7754 (t) REVERT: B 28 TYR cc_start: 0.7615 (m-10) cc_final: 0.7359 (m-10) REVERT: B 41 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6378 (mmtm) REVERT: B 53 ASP cc_start: 0.7593 (t0) cc_final: 0.7377 (t0) REVERT: B 190 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7859 (tpp80) REVERT: B 557 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8147 (mttt) REVERT: B 574 ASP cc_start: 0.7752 (t70) cc_final: 0.7205 (t0) REVERT: B 619 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 646 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7987 (mtm180) REVERT: B 702 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 723 THR cc_start: 0.8417 (p) cc_final: 0.8094 (t) REVERT: B 735 SER cc_start: 0.8607 (m) cc_final: 0.8351 (t) REVERT: B 736 VAL cc_start: 0.8907 (m) cc_final: 0.8591 (t) REVERT: B 740 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (tmm) REVERT: B 776 LYS cc_start: 0.8513 (tttm) cc_final: 0.8121 (tttp) REVERT: B 780 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 811 LYS cc_start: 0.7262 (tttm) cc_final: 0.6782 (tptp) REVERT: B 814 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7797 (mmtt) REVERT: B 868 GLU cc_start: 0.7947 (mp0) cc_final: 0.7674 (mp0) REVERT: B 952 VAL cc_start: 0.8624 (t) cc_final: 0.8397 (m) REVERT: B 979 ASP cc_start: 0.7955 (t70) cc_final: 0.7632 (t70) REVERT: B 1031 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 1038 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8134 (mmtm) REVERT: B 1072 GLU cc_start: 0.8518 (pm20) cc_final: 0.7981 (pm20) REVERT: B 1096 VAL cc_start: 0.8386 (t) cc_final: 0.8059 (m) REVERT: C 24 ARG cc_start: 0.5106 (mtm-85) cc_final: 0.3689 (ttp80) REVERT: C 41 LYS cc_start: 0.6866 (mmpt) cc_final: 0.5764 (mtpp) REVERT: C 100 ILE cc_start: 0.8570 (tp) cc_final: 0.8310 (pp) REVERT: C 155 SER cc_start: 0.8789 (m) cc_final: 0.8444 (t) REVERT: C 156 GLU cc_start: 0.7323 (pm20) cc_final: 0.7046 (pp20) REVERT: C 170 TYR cc_start: 0.8297 (t80) cc_final: 0.8054 (t80) REVERT: C 304 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8199 (mmmm) REVERT: C 305 SER cc_start: 0.8622 (t) cc_final: 0.8281 (p) REVERT: C 308 VAL cc_start: 0.8707 (t) cc_final: 0.8457 (p) REVERT: C 364 ASP cc_start: 0.7358 (t0) cc_final: 0.6538 (p0) REVERT: C 515 PHE cc_start: 0.6851 (m-80) cc_final: 0.6394 (m-80) REVERT: C 574 ASP cc_start: 0.7947 (t0) cc_final: 0.7723 (t0) REVERT: C 577 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8503 (ttm-80) REVERT: C 578 ASP cc_start: 0.8074 (t0) cc_final: 0.7795 (t70) REVERT: C 581 THR cc_start: 0.8114 (m) cc_final: 0.7447 (t) REVERT: C 586 ASP cc_start: 0.7869 (m-30) cc_final: 0.7602 (m-30) REVERT: C 606 ASN cc_start: 0.8919 (m-40) cc_final: 0.8645 (m110) REVERT: C 645 THR cc_start: 0.8414 (m) cc_final: 0.8209 (p) REVERT: C 651 ILE cc_start: 0.8468 (pt) cc_final: 0.8190 (mt) REVERT: C 661 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6992 (tm-30) REVERT: C 748 GLU cc_start: 0.6643 (pp20) cc_final: 0.6247 (pp20) REVERT: C 776 LYS cc_start: 0.8483 (tttm) cc_final: 0.8223 (ttmm) REVERT: C 790 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7720 (mtmm) REVERT: C 811 LYS cc_start: 0.8201 (tttm) cc_final: 0.7817 (tttm) REVERT: C 990 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7018 (mm-30) REVERT: C 1073 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8124 (mmmm) REVERT: C 1105 THR cc_start: 0.8490 (p) cc_final: 0.8139 (t) outliers start: 82 outliers final: 41 residues processed: 640 average time/residue: 1.2317 time to fit residues: 919.9176 Evaluate side-chains 630 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 583 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 107 optimal weight: 0.0770 chunk 210 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 105 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 606 ASN B 710 ASN B 804 GLN B1002 GLN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 949 GLN C 955 ASN C 960 ASN C 978 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130531 restraints weight = 35525.820| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.42 r_work: 0.3528 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25108 Z= 0.132 Angle : 0.582 12.019 34254 Z= 0.295 Chirality : 0.047 0.440 3984 Planarity : 0.004 0.038 4356 Dihedral : 5.852 57.265 4082 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 2.98 % Allowed : 14.85 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3014 helix: 2.55 (0.20), residues: 634 sheet: 0.61 (0.18), residues: 696 loop : -0.82 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 PHE 0.027 0.001 PHE C 541 TYR 0.025 0.001 TYR B 170 ARG 0.010 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 38) link_NAG-ASN : angle 2.95226 ( 114) hydrogen bonds : bond 0.04377 ( 1020) hydrogen bonds : angle 5.42376 ( 2895) SS BOND : bond 0.00340 ( 36) SS BOND : angle 2.09787 ( 72) covalent geometry : bond 0.00297 (25034) covalent geometry : angle 0.54943 (34068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 583 time to evaluate : 2.567 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 26 GLN cc_start: 0.7634 (pt0) cc_final: 0.7412 (pt0) REVERT: A 32 PHE cc_start: 0.9011 (m-80) cc_final: 0.8730 (m-80) REVERT: A 41 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8602 (mttm) REVERT: A 43 PHE cc_start: 0.8765 (t80) cc_final: 0.8519 (t80) REVERT: A 45 SER cc_start: 0.8148 (t) cc_final: 0.7940 (p) REVERT: A 53 ASP cc_start: 0.7352 (t0) cc_final: 0.7056 (t0) REVERT: A 205 SER cc_start: 0.8666 (m) cc_final: 0.8412 (p) REVERT: A 235 ILE cc_start: 0.7010 (tp) cc_final: 0.6774 (tp) REVERT: A 305 SER cc_start: 0.8435 (t) cc_final: 0.8171 (p) REVERT: A 505 HIS cc_start: 0.7455 (m-70) cc_final: 0.6854 (m-70) REVERT: A 554 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 574 ASP cc_start: 0.8048 (t70) cc_final: 0.7643 (t0) REVERT: A 645 THR cc_start: 0.8183 (m) cc_final: 0.7735 (p) REVERT: A 660 TYR cc_start: 0.8586 (m-80) cc_final: 0.8320 (m-80) REVERT: A 714 ILE cc_start: 0.8672 (mm) cc_final: 0.8418 (mp) REVERT: A 723 THR cc_start: 0.8493 (p) cc_final: 0.8279 (m) REVERT: A 725 GLU cc_start: 0.8169 (tt0) cc_final: 0.7898 (tt0) REVERT: A 773 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 814 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8191 (mmmm) REVERT: A 823 PHE cc_start: 0.7096 (m-80) cc_final: 0.6887 (t80) REVERT: A 904 TYR cc_start: 0.7300 (m-10) cc_final: 0.7013 (m-10) REVERT: A 933 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8298 (mtpp) REVERT: A 950 ASP cc_start: 0.7393 (m-30) cc_final: 0.6916 (m-30) REVERT: A 1031 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7388 (tt0) REVERT: A 1045 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7749 (mmtm) REVERT: A 1096 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8115 (m) REVERT: A 1122 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7760 (t) REVERT: B 28 TYR cc_start: 0.7596 (m-10) cc_final: 0.7358 (m-10) REVERT: B 41 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6512 (mmtm) REVERT: B 53 ASP cc_start: 0.7583 (t0) cc_final: 0.7369 (t0) REVERT: B 127 VAL cc_start: 0.8309 (t) cc_final: 0.8039 (m) REVERT: B 190 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7788 (tpp80) REVERT: B 215 ASP cc_start: 0.5024 (OUTLIER) cc_final: 0.4814 (t70) REVERT: B 281 GLU cc_start: 0.8049 (pp20) cc_final: 0.7814 (pp20) REVERT: B 557 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8074 (mttt) REVERT: B 574 ASP cc_start: 0.7732 (t70) cc_final: 0.7162 (t0) REVERT: B 619 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 646 ARG cc_start: 0.8213 (mtm180) cc_final: 0.8003 (mtm110) REVERT: B 658 ASN cc_start: 0.8117 (p0) cc_final: 0.7524 (p0) REVERT: B 702 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 723 THR cc_start: 0.8426 (p) cc_final: 0.8099 (t) REVERT: B 735 SER cc_start: 0.8608 (m) cc_final: 0.8345 (t) REVERT: B 736 VAL cc_start: 0.8884 (m) cc_final: 0.8586 (t) REVERT: B 776 LYS cc_start: 0.8505 (tttm) cc_final: 0.8220 (tttm) REVERT: B 780 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 811 LYS cc_start: 0.7192 (tttm) cc_final: 0.6832 (tppp) REVERT: B 814 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7851 (mmtt) REVERT: B 868 GLU cc_start: 0.7951 (mp0) cc_final: 0.7671 (mp0) REVERT: B 1038 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8126 (mmtm) REVERT: B 1072 GLU cc_start: 0.8491 (pm20) cc_final: 0.7842 (pm20) REVERT: B 1096 VAL cc_start: 0.8354 (t) cc_final: 0.8065 (m) REVERT: C 24 ARG cc_start: 0.5080 (mtm-85) cc_final: 0.3559 (ttp-170) REVERT: C 41 LYS cc_start: 0.6856 (mmpt) cc_final: 0.5656 (mtpp) REVERT: C 100 ILE cc_start: 0.8588 (tp) cc_final: 0.8326 (pp) REVERT: C 155 SER cc_start: 0.8786 (m) cc_final: 0.8438 (t) REVERT: C 156 GLU cc_start: 0.7273 (pm20) cc_final: 0.6998 (pp20) REVERT: C 170 TYR cc_start: 0.8263 (t80) cc_final: 0.8047 (t80) REVERT: C 189 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (tp) REVERT: C 305 SER cc_start: 0.8608 (t) cc_final: 0.8274 (p) REVERT: C 308 VAL cc_start: 0.8710 (t) cc_final: 0.8459 (p) REVERT: C 364 ASP cc_start: 0.7405 (t0) cc_final: 0.6561 (p0) REVERT: C 515 PHE cc_start: 0.6842 (m-80) cc_final: 0.6408 (m-80) REVERT: C 577 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8415 (ttm-80) REVERT: C 578 ASP cc_start: 0.8037 (t0) cc_final: 0.7779 (t70) REVERT: C 581 THR cc_start: 0.8136 (m) cc_final: 0.7543 (t) REVERT: C 586 ASP cc_start: 0.7921 (m-30) cc_final: 0.7696 (m-30) REVERT: C 606 ASN cc_start: 0.8921 (m-40) cc_final: 0.8682 (m-40) REVERT: C 651 ILE cc_start: 0.8385 (pt) cc_final: 0.8114 (mt) REVERT: C 661 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 776 LYS cc_start: 0.8535 (tttm) cc_final: 0.8274 (ttmm) REVERT: C 811 LYS cc_start: 0.8208 (tttm) cc_final: 0.7812 (tttm) REVERT: C 904 TYR cc_start: 0.7140 (m-10) cc_final: 0.6891 (m-10) REVERT: C 1073 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8177 (mmmm) outliers start: 80 outliers final: 43 residues processed: 609 average time/residue: 1.2591 time to fit residues: 895.1762 Evaluate side-chains 614 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 564 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 206 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 245 optimal weight: 0.0670 chunk 147 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN A 913 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN C 121 ASN C 188 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129719 restraints weight = 35830.573| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.43 r_work: 0.3515 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25108 Z= 0.149 Angle : 0.584 11.737 34254 Z= 0.294 Chirality : 0.047 0.416 3984 Planarity : 0.004 0.040 4356 Dihedral : 5.841 58.257 4082 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 3.39 % Allowed : 15.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3014 helix: 2.50 (0.20), residues: 642 sheet: 0.62 (0.18), residues: 688 loop : -0.78 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 PHE 0.028 0.001 PHE C 541 TYR 0.027 0.001 TYR B 170 ARG 0.010 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 38) link_NAG-ASN : angle 3.19738 ( 114) hydrogen bonds : bond 0.04412 ( 1020) hydrogen bonds : angle 5.36903 ( 2895) SS BOND : bond 0.00410 ( 36) SS BOND : angle 1.88556 ( 72) covalent geometry : bond 0.00344 (25034) covalent geometry : angle 0.54872 (34068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 576 time to evaluate : 6.085 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 26 GLN cc_start: 0.7662 (pt0) cc_final: 0.7441 (pt0) REVERT: A 32 PHE cc_start: 0.9012 (m-80) cc_final: 0.8765 (m-80) REVERT: A 41 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8626 (mttm) REVERT: A 43 PHE cc_start: 0.8763 (t80) cc_final: 0.8515 (t80) REVERT: A 53 ASP cc_start: 0.7372 (t0) cc_final: 0.7114 (t0) REVERT: A 205 SER cc_start: 0.8680 (m) cc_final: 0.8421 (p) REVERT: A 305 SER cc_start: 0.8437 (t) cc_final: 0.8169 (p) REVERT: A 505 HIS cc_start: 0.7438 (m-70) cc_final: 0.6808 (m-70) REVERT: A 554 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 564 GLN cc_start: 0.8099 (mp10) cc_final: 0.7753 (mp10) REVERT: A 574 ASP cc_start: 0.8058 (t70) cc_final: 0.7647 (t0) REVERT: A 645 THR cc_start: 0.8216 (m) cc_final: 0.7747 (p) REVERT: A 660 TYR cc_start: 0.8596 (m-80) cc_final: 0.8374 (m-80) REVERT: A 714 ILE cc_start: 0.8644 (mm) cc_final: 0.8413 (mp) REVERT: A 723 THR cc_start: 0.8501 (p) cc_final: 0.8267 (m) REVERT: A 725 GLU cc_start: 0.8165 (tt0) cc_final: 0.7897 (tt0) REVERT: A 773 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 804 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (mm-40) REVERT: A 814 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8179 (mmmm) REVERT: A 823 PHE cc_start: 0.7080 (m-80) cc_final: 0.6853 (t80) REVERT: A 904 TYR cc_start: 0.7457 (m-10) cc_final: 0.6968 (m-10) REVERT: A 933 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8259 (mtpp) REVERT: A 950 ASP cc_start: 0.7456 (m-30) cc_final: 0.6985 (m-30) REVERT: A 1031 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7462 (tt0) REVERT: A 1045 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7788 (mmtm) REVERT: A 1092 GLU cc_start: 0.7227 (pm20) cc_final: 0.6842 (pm20) REVERT: A 1096 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (m) REVERT: A 1122 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7815 (t) REVERT: B 28 TYR cc_start: 0.7626 (m-10) cc_final: 0.7406 (m-10) REVERT: B 41 LYS cc_start: 0.7280 (mmtt) cc_final: 0.6340 (mmtm) REVERT: B 53 ASP cc_start: 0.7612 (t0) cc_final: 0.7391 (t0) REVERT: B 127 VAL cc_start: 0.8343 (t) cc_final: 0.8130 (m) REVERT: B 215 ASP cc_start: 0.5032 (OUTLIER) cc_final: 0.4812 (t70) REVERT: B 509 ARG cc_start: 0.6702 (mtt180) cc_final: 0.6433 (mtt180) REVERT: B 557 LYS cc_start: 0.8409 (ptpt) cc_final: 0.8044 (mttt) REVERT: B 574 ASP cc_start: 0.7734 (t70) cc_final: 0.7086 (t0) REVERT: B 619 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 702 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 723 THR cc_start: 0.8432 (p) cc_final: 0.8109 (t) REVERT: B 735 SER cc_start: 0.8614 (m) cc_final: 0.8349 (t) REVERT: B 736 VAL cc_start: 0.8880 (m) cc_final: 0.8572 (t) REVERT: B 740 MET cc_start: 0.8608 (mmm) cc_final: 0.8239 (tpt) REVERT: B 776 LYS cc_start: 0.8509 (tttm) cc_final: 0.8216 (tttm) REVERT: B 780 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 811 LYS cc_start: 0.7209 (tttm) cc_final: 0.6665 (tttm) REVERT: B 814 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7817 (mmtt) REVERT: B 868 GLU cc_start: 0.7974 (mp0) cc_final: 0.7647 (mp0) REVERT: B 1038 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8118 (mmtm) REVERT: B 1072 GLU cc_start: 0.8523 (pm20) cc_final: 0.7842 (pm20) REVERT: B 1096 VAL cc_start: 0.8391 (t) cc_final: 0.8106 (m) REVERT: B 1122 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8386 (t) REVERT: C 24 ARG cc_start: 0.4951 (mtm-85) cc_final: 0.3518 (ttp-170) REVERT: C 33 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 41 LYS cc_start: 0.6887 (mmpt) cc_final: 0.5674 (mtpp) REVERT: C 100 ILE cc_start: 0.8600 (tp) cc_final: 0.8353 (pp) REVERT: C 155 SER cc_start: 0.8772 (m) cc_final: 0.8428 (t) REVERT: C 156 GLU cc_start: 0.7241 (pm20) cc_final: 0.6917 (pp20) REVERT: C 189 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (tp) REVERT: C 305 SER cc_start: 0.8612 (t) cc_final: 0.8272 (p) REVERT: C 308 VAL cc_start: 0.8709 (t) cc_final: 0.8455 (p) REVERT: C 577 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8434 (ttm-80) REVERT: C 581 THR cc_start: 0.8144 (m) cc_final: 0.7617 (t) REVERT: C 586 ASP cc_start: 0.7895 (m-30) cc_final: 0.7670 (m-30) REVERT: C 606 ASN cc_start: 0.8923 (m-40) cc_final: 0.8692 (m-40) REVERT: C 651 ILE cc_start: 0.8370 (pt) cc_final: 0.8097 (mt) REVERT: C 661 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 748 GLU cc_start: 0.6460 (pp20) cc_final: 0.6006 (pp20) REVERT: C 776 LYS cc_start: 0.8541 (tttm) cc_final: 0.8272 (ttmm) REVERT: C 790 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8117 (mtmm) REVERT: C 900 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: C 904 TYR cc_start: 0.7071 (m-10) cc_final: 0.6778 (m-10) REVERT: C 1073 LYS cc_start: 0.8397 (mmmm) cc_final: 0.8173 (mmmm) outliers start: 91 outliers final: 49 residues processed: 611 average time/residue: 1.2851 time to fit residues: 919.0878 Evaluate side-chains 621 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 562 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 6 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN A 965 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 606 ASN B 710 ASN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127757 restraints weight = 35943.090| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.43 r_work: 0.3485 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25108 Z= 0.218 Angle : 0.632 13.157 34254 Z= 0.318 Chirality : 0.048 0.416 3984 Planarity : 0.004 0.042 4356 Dihedral : 5.709 58.561 4080 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.36 % Allowed : 16.34 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3014 helix: 2.38 (0.20), residues: 634 sheet: 0.62 (0.18), residues: 700 loop : -0.85 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS B1058 PHE 0.029 0.002 PHE C 541 TYR 0.027 0.002 TYR B 279 ARG 0.007 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 38) link_NAG-ASN : angle 3.19009 ( 114) hydrogen bonds : bond 0.04967 ( 1020) hydrogen bonds : angle 5.47806 ( 2895) SS BOND : bond 0.00459 ( 36) SS BOND : angle 2.04333 ( 72) covalent geometry : bond 0.00507 (25034) covalent geometry : angle 0.59856 (34068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 576 time to evaluate : 2.605 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: symmetry clash REVERT: A 26 GLN cc_start: 0.7700 (pt0) cc_final: 0.7483 (pt0) REVERT: A 32 PHE cc_start: 0.8994 (m-80) cc_final: 0.8724 (m-80) REVERT: A 41 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8666 (mttm) REVERT: A 43 PHE cc_start: 0.8818 (t80) cc_final: 0.8560 (t80) REVERT: A 205 SER cc_start: 0.8650 (m) cc_final: 0.8426 (p) REVERT: A 305 SER cc_start: 0.8499 (t) cc_final: 0.8219 (p) REVERT: A 371 PHE cc_start: 0.7216 (m-80) cc_final: 0.7013 (m-80) REVERT: A 505 HIS cc_start: 0.7528 (m-70) cc_final: 0.6920 (m-70) REVERT: A 554 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 564 GLN cc_start: 0.8240 (mp10) cc_final: 0.7857 (mp10) REVERT: A 574 ASP cc_start: 0.8034 (t70) cc_final: 0.7609 (t0) REVERT: A 725 GLU cc_start: 0.8257 (tt0) cc_final: 0.7958 (tt0) REVERT: A 765 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8081 (ttm170) REVERT: A 804 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8345 (mm-40) REVERT: A 814 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8190 (mmmm) REVERT: A 904 TYR cc_start: 0.7692 (m-10) cc_final: 0.7083 (m-10) REVERT: A 933 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8253 (mtpp) REVERT: A 950 ASP cc_start: 0.7557 (m-30) cc_final: 0.7075 (m-30) REVERT: A 957 GLN cc_start: 0.8038 (tp40) cc_final: 0.7812 (tp40) REVERT: A 1045 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7815 (mmtm) REVERT: A 1122 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7871 (t) REVERT: B 28 TYR cc_start: 0.7682 (m-10) cc_final: 0.7460 (m-80) REVERT: B 41 LYS cc_start: 0.7344 (mmtt) cc_final: 0.6361 (mmtm) REVERT: B 53 ASP cc_start: 0.7671 (t0) cc_final: 0.7447 (t0) REVERT: B 509 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6581 (mtt180) REVERT: B 557 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8205 (mtmt) REVERT: B 574 ASP cc_start: 0.7700 (t70) cc_final: 0.7117 (t0) REVERT: B 619 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 702 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 723 THR cc_start: 0.8462 (p) cc_final: 0.8134 (t) REVERT: B 735 SER cc_start: 0.8677 (m) cc_final: 0.8403 (t) REVERT: B 736 VAL cc_start: 0.8883 (m) cc_final: 0.8557 (t) REVERT: B 740 MET cc_start: 0.8602 (mmm) cc_final: 0.8212 (tpt) REVERT: B 776 LYS cc_start: 0.8546 (tttm) cc_final: 0.8209 (tttm) REVERT: B 780 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 811 LYS cc_start: 0.7247 (tttm) cc_final: 0.6713 (tttm) REVERT: B 814 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7842 (mmtt) REVERT: B 868 GLU cc_start: 0.7933 (mp0) cc_final: 0.7570 (mp0) REVERT: B 902 MET cc_start: 0.8449 (tpp) cc_final: 0.8231 (mmp) REVERT: B 1038 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8128 (mmtm) REVERT: B 1096 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 1116 THR cc_start: 0.8174 (p) cc_final: 0.7822 (t) REVERT: C 33 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 41 LYS cc_start: 0.6917 (mmpt) cc_final: 0.5541 (mtpp) REVERT: C 100 ILE cc_start: 0.8600 (tp) cc_final: 0.8341 (pp) REVERT: C 155 SER cc_start: 0.8796 (m) cc_final: 0.8486 (t) REVERT: C 156 GLU cc_start: 0.7329 (pm20) cc_final: 0.7042 (pp20) REVERT: C 189 LEU cc_start: 0.8695 (tt) cc_final: 0.8419 (tp) REVERT: C 305 SER cc_start: 0.8634 (t) cc_final: 0.8301 (p) REVERT: C 308 VAL cc_start: 0.8697 (t) cc_final: 0.8436 (p) REVERT: C 581 THR cc_start: 0.8033 (m) cc_final: 0.7643 (t) REVERT: C 586 ASP cc_start: 0.7857 (m-30) cc_final: 0.7651 (m-30) REVERT: C 606 ASN cc_start: 0.8932 (m-40) cc_final: 0.8705 (m-40) REVERT: C 651 ILE cc_start: 0.8401 (pt) cc_final: 0.8192 (mt) REVERT: C 661 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 748 GLU cc_start: 0.6568 (pp20) cc_final: 0.6023 (pp20) REVERT: C 776 LYS cc_start: 0.8527 (tttm) cc_final: 0.8282 (ttmm) REVERT: C 900 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8054 (mtt) REVERT: C 904 TYR cc_start: 0.7051 (m-10) cc_final: 0.6798 (m-10) REVERT: C 957 GLN cc_start: 0.8433 (tt0) cc_final: 0.8228 (tt0) REVERT: C 990 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7030 (mm-30) REVERT: C 1073 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8181 (mmmm) outliers start: 90 outliers final: 56 residues processed: 607 average time/residue: 1.2309 time to fit residues: 868.1859 Evaluate side-chains 626 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 564 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 249 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 196 ASN B 239 GLN B 710 ASN C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 422 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127288 restraints weight = 35698.382| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.42 r_work: 0.3478 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25108 Z= 0.227 Angle : 0.632 11.301 34254 Z= 0.319 Chirality : 0.048 0.413 3984 Planarity : 0.004 0.054 4356 Dihedral : 5.665 57.897 4080 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 3.47 % Allowed : 17.98 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3014 helix: 2.30 (0.20), residues: 636 sheet: 0.55 (0.18), residues: 710 loop : -0.90 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.005 0.001 HIS B 49 PHE 0.028 0.002 PHE B 168 TYR 0.031 0.002 TYR C 170 ARG 0.006 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 38) link_NAG-ASN : angle 3.18949 ( 114) hydrogen bonds : bond 0.05001 ( 1020) hydrogen bonds : angle 5.48540 ( 2895) SS BOND : bond 0.00488 ( 36) SS BOND : angle 1.97113 ( 72) covalent geometry : bond 0.00531 (25034) covalent geometry : angle 0.59982 (34068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 574 time to evaluate : 2.589 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 26 GLN cc_start: 0.7720 (pt0) cc_final: 0.7509 (pt0) REVERT: A 32 PHE cc_start: 0.8989 (m-80) cc_final: 0.8745 (m-80) REVERT: A 41 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8693 (mttm) REVERT: A 43 PHE cc_start: 0.8779 (t80) cc_final: 0.8534 (t80) REVERT: A 205 SER cc_start: 0.8663 (m) cc_final: 0.8443 (p) REVERT: A 305 SER cc_start: 0.8521 (t) cc_final: 0.8230 (p) REVERT: A 433 VAL cc_start: 0.8990 (t) cc_final: 0.8606 (m) REVERT: A 554 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 574 ASP cc_start: 0.8021 (t70) cc_final: 0.7593 (t0) REVERT: A 645 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 660 TYR cc_start: 0.8676 (m-10) cc_final: 0.8359 (m-80) REVERT: A 725 GLU cc_start: 0.8249 (tt0) cc_final: 0.7939 (tt0) REVERT: A 765 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8096 (ttm170) REVERT: A 814 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8189 (mmmm) REVERT: A 933 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8243 (mtpp) REVERT: A 950 ASP cc_start: 0.7546 (m-30) cc_final: 0.7058 (m-30) REVERT: A 957 GLN cc_start: 0.8039 (tp40) cc_final: 0.7809 (tp40) REVERT: A 998 THR cc_start: 0.8316 (t) cc_final: 0.8096 (p) REVERT: A 1045 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7788 (mmtm) REVERT: A 1100 THR cc_start: 0.8314 (m) cc_final: 0.8063 (p) REVERT: A 1111 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7862 (tt0) REVERT: A 1122 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (t) REVERT: B 41 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6456 (mmtm) REVERT: B 53 ASP cc_start: 0.7633 (t0) cc_final: 0.7416 (t0) REVERT: B 509 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6543 (mtt180) REVERT: B 574 ASP cc_start: 0.7718 (t70) cc_final: 0.7166 (t0) REVERT: B 619 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 702 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 723 THR cc_start: 0.8476 (p) cc_final: 0.8139 (t) REVERT: B 735 SER cc_start: 0.8710 (m) cc_final: 0.8464 (t) REVERT: B 736 VAL cc_start: 0.8891 (m) cc_final: 0.8565 (t) REVERT: B 740 MET cc_start: 0.8586 (mmm) cc_final: 0.8272 (tpt) REVERT: B 776 LYS cc_start: 0.8565 (tttm) cc_final: 0.8281 (tttm) REVERT: B 780 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 811 LYS cc_start: 0.7270 (tttm) cc_final: 0.6752 (tttm) REVERT: B 814 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7845 (mmtt) REVERT: B 868 GLU cc_start: 0.7879 (mp0) cc_final: 0.7475 (mp0) REVERT: B 902 MET cc_start: 0.8437 (tpp) cc_final: 0.8204 (mmp) REVERT: B 1038 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8146 (mmtm) REVERT: B 1096 VAL cc_start: 0.8524 (t) cc_final: 0.8238 (m) REVERT: B 1116 THR cc_start: 0.8152 (p) cc_final: 0.7800 (t) REVERT: C 33 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (p) REVERT: C 41 LYS cc_start: 0.6905 (mmpt) cc_final: 0.5561 (mtpp) REVERT: C 100 ILE cc_start: 0.8596 (tp) cc_final: 0.8349 (pp) REVERT: C 155 SER cc_start: 0.8802 (m) cc_final: 0.8501 (t) REVERT: C 156 GLU cc_start: 0.7316 (pm20) cc_final: 0.7043 (pp20) REVERT: C 189 LEU cc_start: 0.8715 (tt) cc_final: 0.8437 (tp) REVERT: C 200 TYR cc_start: 0.8360 (m-10) cc_final: 0.8044 (m-10) REVERT: C 305 SER cc_start: 0.8663 (t) cc_final: 0.8319 (p) REVERT: C 308 VAL cc_start: 0.8695 (t) cc_final: 0.8432 (p) REVERT: C 581 THR cc_start: 0.8071 (m) cc_final: 0.7678 (t) REVERT: C 606 ASN cc_start: 0.8940 (m-40) cc_final: 0.8713 (m-40) REVERT: C 651 ILE cc_start: 0.8397 (pt) cc_final: 0.8189 (mt) REVERT: C 661 GLU cc_start: 0.7262 (tm-30) cc_final: 0.7025 (tm-30) REVERT: C 776 LYS cc_start: 0.8539 (tttm) cc_final: 0.8296 (ttmm) REVERT: C 900 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8075 (mtt) REVERT: C 904 TYR cc_start: 0.7081 (m-10) cc_final: 0.6811 (m-10) REVERT: C 957 GLN cc_start: 0.8446 (tt0) cc_final: 0.8233 (tt0) REVERT: C 1073 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8182 (mmmm) outliers start: 93 outliers final: 61 residues processed: 611 average time/residue: 1.5423 time to fit residues: 1104.9764 Evaluate side-chains 626 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 560 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 259 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 284 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 196 ASN B 239 GLN B 710 ASN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127566 restraints weight = 35787.321| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.44 r_work: 0.3493 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25108 Z= 0.179 Angle : 0.621 10.600 34254 Z= 0.313 Chirality : 0.047 0.406 3984 Planarity : 0.004 0.041 4356 Dihedral : 5.541 59.498 4080 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.13 % Allowed : 19.17 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3014 helix: 2.40 (0.20), residues: 641 sheet: 0.61 (0.19), residues: 690 loop : -0.87 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.003 0.001 HIS B 49 PHE 0.028 0.002 PHE C 541 TYR 0.029 0.002 TYR A 501 ARG 0.006 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 38) link_NAG-ASN : angle 3.13967 ( 114) hydrogen bonds : bond 0.04717 ( 1020) hydrogen bonds : angle 5.43861 ( 2895) SS BOND : bond 0.00468 ( 36) SS BOND : angle 1.79912 ( 72) covalent geometry : bond 0.00418 (25034) covalent geometry : angle 0.58961 (34068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 567 time to evaluate : 2.432 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 26 GLN cc_start: 0.7712 (pt0) cc_final: 0.7494 (pt0) REVERT: A 32 PHE cc_start: 0.9003 (m-80) cc_final: 0.8728 (m-80) REVERT: A 41 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8691 (mttm) REVERT: A 43 PHE cc_start: 0.8761 (t80) cc_final: 0.8525 (t80) REVERT: A 53 ASP cc_start: 0.7378 (t0) cc_final: 0.7079 (t70) REVERT: A 205 SER cc_start: 0.8681 (m) cc_final: 0.8450 (p) REVERT: A 305 SER cc_start: 0.8522 (t) cc_final: 0.8233 (p) REVERT: A 554 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 571 ASP cc_start: 0.7539 (t0) cc_final: 0.7119 (t0) REVERT: A 574 ASP cc_start: 0.8020 (t70) cc_final: 0.7592 (t0) REVERT: A 645 THR cc_start: 0.8358 (m) cc_final: 0.7893 (p) REVERT: A 660 TYR cc_start: 0.8674 (m-80) cc_final: 0.8319 (m-80) REVERT: A 725 GLU cc_start: 0.8250 (tt0) cc_final: 0.7947 (tt0) REVERT: A 765 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8040 (ttm170) REVERT: A 814 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8255 (mppt) REVERT: A 933 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8231 (mtpp) REVERT: A 950 ASP cc_start: 0.7506 (m-30) cc_final: 0.7019 (m-30) REVERT: A 998 THR cc_start: 0.8310 (t) cc_final: 0.8083 (p) REVERT: A 1045 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7757 (mmtm) REVERT: A 1100 THR cc_start: 0.8303 (m) cc_final: 0.8059 (p) REVERT: A 1122 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7868 (t) REVERT: B 41 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6444 (mmtm) REVERT: B 53 ASP cc_start: 0.7581 (t0) cc_final: 0.7354 (t0) REVERT: B 127 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8133 (m) REVERT: B 574 ASP cc_start: 0.7722 (t70) cc_final: 0.7176 (t0) REVERT: B 619 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 702 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 723 THR cc_start: 0.8485 (p) cc_final: 0.8150 (t) REVERT: B 735 SER cc_start: 0.8689 (m) cc_final: 0.8404 (t) REVERT: B 736 VAL cc_start: 0.8873 (m) cc_final: 0.8550 (t) REVERT: B 740 MET cc_start: 0.8541 (mmm) cc_final: 0.8235 (ttt) REVERT: B 776 LYS cc_start: 0.8542 (tttm) cc_final: 0.8131 (tttp) REVERT: B 780 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 814 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7859 (mmtt) REVERT: B 1038 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8136 (mmtm) REVERT: B 1096 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (m) REVERT: B 1116 THR cc_start: 0.8122 (p) cc_final: 0.7762 (t) REVERT: B 1128 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8424 (t) REVERT: C 33 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8182 (p) REVERT: C 41 LYS cc_start: 0.6878 (mmpt) cc_final: 0.5565 (mtpp) REVERT: C 100 ILE cc_start: 0.8582 (tp) cc_final: 0.8342 (pp) REVERT: C 155 SER cc_start: 0.8823 (m) cc_final: 0.8531 (t) REVERT: C 156 GLU cc_start: 0.7326 (pm20) cc_final: 0.7057 (pp20) REVERT: C 189 LEU cc_start: 0.8737 (tt) cc_final: 0.8457 (tp) REVERT: C 304 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8287 (mmtp) REVERT: C 305 SER cc_start: 0.8646 (t) cc_final: 0.8307 (p) REVERT: C 308 VAL cc_start: 0.8690 (t) cc_final: 0.8431 (p) REVERT: C 577 ARG cc_start: 0.8808 (ttm110) cc_final: 0.8603 (ttm-80) REVERT: C 578 ASP cc_start: 0.7903 (t0) cc_final: 0.7564 (t70) REVERT: C 580 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: C 581 THR cc_start: 0.8093 (m) cc_final: 0.7510 (t) REVERT: C 606 ASN cc_start: 0.8929 (m-40) cc_final: 0.8704 (m-40) REVERT: C 651 ILE cc_start: 0.8404 (pt) cc_final: 0.8159 (mt) REVERT: C 661 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 776 LYS cc_start: 0.8506 (tttm) cc_final: 0.8260 (ttmm) REVERT: C 900 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7985 (mtt) REVERT: C 904 TYR cc_start: 0.7087 (m-10) cc_final: 0.6869 (m-10) REVERT: C 957 GLN cc_start: 0.8459 (tt0) cc_final: 0.8256 (tt0) REVERT: C 1073 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8188 (mmmm) outliers start: 84 outliers final: 57 residues processed: 598 average time/residue: 1.4187 time to fit residues: 985.8492 Evaluate side-chains 615 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 550 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 34 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 42 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 274 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 239 GLN B 710 ASN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128647 restraints weight = 35841.023| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.42 r_work: 0.3500 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25108 Z= 0.144 Angle : 0.608 11.179 34254 Z= 0.305 Chirality : 0.047 0.414 3984 Planarity : 0.004 0.042 4356 Dihedral : 5.458 59.242 4080 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.80 % Allowed : 19.77 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3014 helix: 2.45 (0.20), residues: 650 sheet: 0.60 (0.19), residues: 690 loop : -0.82 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS C 69 PHE 0.031 0.001 PHE C 541 TYR 0.032 0.001 TYR C 170 ARG 0.007 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 38) link_NAG-ASN : angle 3.08704 ( 114) hydrogen bonds : bond 0.04417 ( 1020) hydrogen bonds : angle 5.34586 ( 2895) SS BOND : bond 0.00584 ( 36) SS BOND : angle 1.62685 ( 72) covalent geometry : bond 0.00334 (25034) covalent geometry : angle 0.57793 (34068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 556 time to evaluate : 2.750 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: symmetry clash REVERT: A 26 GLN cc_start: 0.7683 (pt0) cc_final: 0.7452 (pt0) REVERT: A 32 PHE cc_start: 0.9002 (m-80) cc_final: 0.8733 (m-80) REVERT: A 41 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8661 (mttm) REVERT: A 43 PHE cc_start: 0.8745 (t80) cc_final: 0.8514 (t80) REVERT: A 53 ASP cc_start: 0.7375 (t0) cc_final: 0.7070 (t70) REVERT: A 205 SER cc_start: 0.8698 (m) cc_final: 0.8459 (p) REVERT: A 305 SER cc_start: 0.8506 (t) cc_final: 0.8220 (p) REVERT: A 554 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 571 ASP cc_start: 0.7533 (t0) cc_final: 0.7119 (t0) REVERT: A 574 ASP cc_start: 0.8013 (t70) cc_final: 0.7589 (t0) REVERT: A 645 THR cc_start: 0.8398 (m) cc_final: 0.7961 (p) REVERT: A 660 TYR cc_start: 0.8652 (m-80) cc_final: 0.8356 (m-80) REVERT: A 725 GLU cc_start: 0.8190 (tt0) cc_final: 0.7911 (tt0) REVERT: A 735 SER cc_start: 0.8816 (m) cc_final: 0.8562 (t) REVERT: A 814 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8243 (mppt) REVERT: A 933 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8240 (mtpp) REVERT: A 950 ASP cc_start: 0.7445 (m-30) cc_final: 0.6960 (m-30) REVERT: A 998 THR cc_start: 0.8307 (t) cc_final: 0.8085 (p) REVERT: A 1045 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7757 (mmtm) REVERT: A 1100 THR cc_start: 0.8293 (m) cc_final: 0.8062 (p) REVERT: A 1107 ARG cc_start: 0.8320 (mtt90) cc_final: 0.8081 (mtt90) REVERT: A 1122 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7872 (t) REVERT: B 41 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6134 (mmtp) REVERT: B 53 ASP cc_start: 0.7573 (t0) cc_final: 0.7352 (t0) REVERT: B 574 ASP cc_start: 0.7673 (t70) cc_final: 0.7141 (t0) REVERT: B 619 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 702 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 723 THR cc_start: 0.8477 (p) cc_final: 0.8143 (t) REVERT: B 735 SER cc_start: 0.8673 (m) cc_final: 0.8403 (t) REVERT: B 736 VAL cc_start: 0.8868 (m) cc_final: 0.8550 (t) REVERT: B 740 MET cc_start: 0.8546 (mmm) cc_final: 0.8272 (ttt) REVERT: B 776 LYS cc_start: 0.8551 (tttm) cc_final: 0.8151 (tttp) REVERT: B 780 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 814 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7868 (mmtt) REVERT: B 902 MET cc_start: 0.8390 (tpp) cc_final: 0.8174 (mmp) REVERT: B 1038 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8117 (mmtm) REVERT: B 1096 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8158 (m) REVERT: B 1116 THR cc_start: 0.8103 (p) cc_final: 0.7766 (t) REVERT: B 1128 VAL cc_start: 0.8659 (p) cc_final: 0.8437 (t) REVERT: C 33 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 41 LYS cc_start: 0.6876 (mmpt) cc_final: 0.5697 (mtpp) REVERT: C 100 ILE cc_start: 0.8581 (tp) cc_final: 0.8341 (pp) REVERT: C 155 SER cc_start: 0.8792 (m) cc_final: 0.8490 (t) REVERT: C 156 GLU cc_start: 0.7270 (pm20) cc_final: 0.6998 (pp20) REVERT: C 189 LEU cc_start: 0.8741 (tt) cc_final: 0.8463 (tp) REVERT: C 200 TYR cc_start: 0.8313 (m-10) cc_final: 0.8062 (m-10) REVERT: C 304 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8249 (mmtp) REVERT: C 305 SER cc_start: 0.8631 (t) cc_final: 0.8292 (p) REVERT: C 308 VAL cc_start: 0.8703 (t) cc_final: 0.8451 (p) REVERT: C 564 GLN cc_start: 0.7995 (mp-120) cc_final: 0.7519 (mp-120) REVERT: C 577 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8572 (ttm-80) REVERT: C 578 ASP cc_start: 0.7922 (t0) cc_final: 0.7561 (t70) REVERT: C 580 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7669 (mp10) REVERT: C 581 THR cc_start: 0.8089 (m) cc_final: 0.7495 (t) REVERT: C 583 GLU cc_start: 0.7685 (pm20) cc_final: 0.7378 (pm20) REVERT: C 606 ASN cc_start: 0.8925 (m-40) cc_final: 0.8693 (m-40) REVERT: C 651 ILE cc_start: 0.8363 (pt) cc_final: 0.8137 (mt) REVERT: C 661 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6944 (tm-30) REVERT: C 776 LYS cc_start: 0.8512 (tttm) cc_final: 0.8249 (ttmm) REVERT: C 900 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: C 904 TYR cc_start: 0.7025 (m-10) cc_final: 0.6811 (m-10) REVERT: C 1073 LYS cc_start: 0.8412 (mmmm) cc_final: 0.8200 (mmmm) outliers start: 75 outliers final: 49 residues processed: 585 average time/residue: 1.4702 time to fit residues: 999.5689 Evaluate side-chains 600 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 545 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 194 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 196 ASN B 239 GLN B 710 ASN B 755 GLN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 542 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN C 978 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127806 restraints weight = 36015.713| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.43 r_work: 0.3484 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25108 Z= 0.188 Angle : 0.635 11.261 34254 Z= 0.319 Chirality : 0.048 0.399 3984 Planarity : 0.004 0.041 4356 Dihedral : 5.483 59.981 4080 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.76 % Allowed : 20.07 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3014 helix: 2.38 (0.20), residues: 651 sheet: 0.62 (0.19), residues: 694 loop : -0.86 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 436 HIS 0.005 0.001 HIS B 339 PHE 0.032 0.002 PHE C 541 TYR 0.023 0.001 TYR C 28 ARG 0.008 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 38) link_NAG-ASN : angle 3.07748 ( 114) hydrogen bonds : bond 0.04677 ( 1020) hydrogen bonds : angle 5.36738 ( 2895) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.90661 ( 72) covalent geometry : bond 0.00442 (25034) covalent geometry : angle 0.60526 (34068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 557 time to evaluate : 2.910 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 26 GLN cc_start: 0.7704 (pt0) cc_final: 0.7471 (pt0) REVERT: A 32 PHE cc_start: 0.8998 (m-80) cc_final: 0.8773 (m-80) REVERT: A 41 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8671 (mttm) REVERT: A 205 SER cc_start: 0.8688 (m) cc_final: 0.8434 (p) REVERT: A 305 SER cc_start: 0.8518 (t) cc_final: 0.8228 (p) REVERT: A 335 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 402 ILE cc_start: 0.8578 (mm) cc_final: 0.8359 (mp) REVERT: A 554 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 571 ASP cc_start: 0.7562 (t0) cc_final: 0.7143 (t0) REVERT: A 574 ASP cc_start: 0.8033 (t70) cc_final: 0.7609 (t0) REVERT: A 645 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8002 (p) REVERT: A 660 TYR cc_start: 0.8658 (m-80) cc_final: 0.8285 (m-80) REVERT: A 725 GLU cc_start: 0.8230 (tt0) cc_final: 0.7926 (tt0) REVERT: A 735 SER cc_start: 0.8861 (m) cc_final: 0.8601 (t) REVERT: A 814 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8267 (mppt) REVERT: A 823 PHE cc_start: 0.7278 (t80) cc_final: 0.6888 (m-80) REVERT: A 933 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8223 (mtpp) REVERT: A 950 ASP cc_start: 0.7515 (m-30) cc_final: 0.7030 (m-30) REVERT: A 998 THR cc_start: 0.8332 (t) cc_final: 0.8104 (p) REVERT: A 1045 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7782 (mmtm) REVERT: A 1122 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7903 (t) REVERT: B 41 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6196 (mmtp) REVERT: B 53 ASP cc_start: 0.7611 (t0) cc_final: 0.7395 (t0) REVERT: B 509 ARG cc_start: 0.6805 (mtt180) cc_final: 0.6415 (mtt-85) REVERT: B 574 ASP cc_start: 0.7706 (t70) cc_final: 0.7178 (t0) REVERT: B 619 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 702 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 723 THR cc_start: 0.8484 (p) cc_final: 0.8154 (t) REVERT: B 735 SER cc_start: 0.8687 (m) cc_final: 0.8411 (t) REVERT: B 736 VAL cc_start: 0.8881 (m) cc_final: 0.8557 (t) REVERT: B 740 MET cc_start: 0.8570 (mmm) cc_final: 0.8302 (ttt) REVERT: B 776 LYS cc_start: 0.8573 (tttm) cc_final: 0.8287 (tttp) REVERT: B 814 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7855 (mmtt) REVERT: B 868 GLU cc_start: 0.7897 (mp0) cc_final: 0.7476 (mp0) REVERT: B 902 MET cc_start: 0.8426 (tpp) cc_final: 0.8192 (mmp) REVERT: B 1038 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8137 (mmtm) REVERT: B 1096 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8202 (m) REVERT: B 1116 THR cc_start: 0.8121 (p) cc_final: 0.7770 (t) REVERT: B 1128 VAL cc_start: 0.8698 (p) cc_final: 0.8438 (t) REVERT: C 33 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8157 (p) REVERT: C 41 LYS cc_start: 0.6877 (mmpt) cc_final: 0.5556 (mtpp) REVERT: C 100 ILE cc_start: 0.8598 (tp) cc_final: 0.8372 (pp) REVERT: C 155 SER cc_start: 0.8810 (m) cc_final: 0.8516 (t) REVERT: C 156 GLU cc_start: 0.7332 (pm20) cc_final: 0.7044 (pp20) REVERT: C 189 LEU cc_start: 0.8750 (tt) cc_final: 0.8488 (tp) REVERT: C 200 TYR cc_start: 0.8328 (m-10) cc_final: 0.8099 (m-10) REVERT: C 304 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8244 (mmtp) REVERT: C 305 SER cc_start: 0.8626 (t) cc_final: 0.8285 (p) REVERT: C 308 VAL cc_start: 0.8701 (t) cc_final: 0.8447 (p) REVERT: C 577 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8578 (ttm-80) REVERT: C 578 ASP cc_start: 0.7952 (t0) cc_final: 0.7603 (t70) REVERT: C 580 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: C 581 THR cc_start: 0.8090 (m) cc_final: 0.7500 (t) REVERT: C 583 GLU cc_start: 0.7723 (pm20) cc_final: 0.7406 (pm20) REVERT: C 606 ASN cc_start: 0.8933 (m-40) cc_final: 0.8706 (m-40) REVERT: C 651 ILE cc_start: 0.8375 (pt) cc_final: 0.8167 (mt) REVERT: C 661 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6981 (tm-30) REVERT: C 748 GLU cc_start: 0.6470 (pp20) cc_final: 0.6020 (pp20) REVERT: C 776 LYS cc_start: 0.8535 (tttm) cc_final: 0.8284 (ttmm) REVERT: C 900 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7995 (mtt) REVERT: C 904 TYR cc_start: 0.7057 (m-10) cc_final: 0.6842 (m-10) REVERT: C 918 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 957 GLN cc_start: 0.8474 (tt0) cc_final: 0.8248 (tt0) REVERT: C 990 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7098 (mm-30) REVERT: C 1031 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7663 (mp0) REVERT: C 1073 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8233 (mmmm) outliers start: 74 outliers final: 53 residues processed: 586 average time/residue: 1.4005 time to fit residues: 955.3967 Evaluate side-chains 605 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 543 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 291 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 151 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 239 GLN B 710 ASN B 755 GLN B1135 ASN C 26 GLN C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 564 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN C 978 ASN C1036 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128073 restraints weight = 35921.467| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.43 r_work: 0.3489 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25108 Z= 0.164 Angle : 0.633 11.710 34254 Z= 0.319 Chirality : 0.047 0.377 3984 Planarity : 0.004 0.040 4356 Dihedral : 5.453 59.139 4080 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.65 % Allowed : 20.29 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3014 helix: 2.41 (0.20), residues: 648 sheet: 0.58 (0.19), residues: 683 loop : -0.85 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 436 HIS 0.003 0.001 HIS A 66 PHE 0.033 0.002 PHE C 168 TYR 0.035 0.001 TYR C 170 ARG 0.007 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 38) link_NAG-ASN : angle 3.09620 ( 114) hydrogen bonds : bond 0.04522 ( 1020) hydrogen bonds : angle 5.36043 ( 2895) SS BOND : bond 0.00412 ( 36) SS BOND : angle 1.85376 ( 72) covalent geometry : bond 0.00387 (25034) covalent geometry : angle 0.60308 (34068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 547 time to evaluate : 2.624 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 26 GLN cc_start: 0.7698 (pt0) cc_final: 0.7488 (pt0) REVERT: A 32 PHE cc_start: 0.9004 (m-80) cc_final: 0.8763 (m-80) REVERT: A 41 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8675 (mttm) REVERT: A 205 SER cc_start: 0.8716 (m) cc_final: 0.8461 (p) REVERT: A 305 SER cc_start: 0.8481 (t) cc_final: 0.8194 (p) REVERT: A 335 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 433 VAL cc_start: 0.8991 (t) cc_final: 0.8617 (m) REVERT: A 554 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 571 ASP cc_start: 0.7557 (t0) cc_final: 0.7136 (t0) REVERT: A 574 ASP cc_start: 0.8037 (t70) cc_final: 0.7620 (t0) REVERT: A 645 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 660 TYR cc_start: 0.8623 (m-80) cc_final: 0.8344 (m-80) REVERT: A 725 GLU cc_start: 0.8192 (tt0) cc_final: 0.7891 (tt0) REVERT: A 735 SER cc_start: 0.8864 (m) cc_final: 0.8601 (t) REVERT: A 814 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8269 (mppt) REVERT: A 933 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8212 (mtpp) REVERT: A 950 ASP cc_start: 0.7483 (m-30) cc_final: 0.7002 (m-30) REVERT: A 998 THR cc_start: 0.8324 (t) cc_final: 0.8097 (p) REVERT: A 1045 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7774 (mmtm) REVERT: A 1122 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 41 LYS cc_start: 0.7420 (mmtt) cc_final: 0.6192 (mmtp) REVERT: B 53 ASP cc_start: 0.7584 (t0) cc_final: 0.7364 (t0) REVERT: B 574 ASP cc_start: 0.7699 (t70) cc_final: 0.7180 (t0) REVERT: B 619 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 702 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 723 THR cc_start: 0.8478 (p) cc_final: 0.8148 (t) REVERT: B 735 SER cc_start: 0.8694 (m) cc_final: 0.8420 (t) REVERT: B 736 VAL cc_start: 0.8874 (m) cc_final: 0.8556 (t) REVERT: B 740 MET cc_start: 0.8539 (mmm) cc_final: 0.8280 (ttt) REVERT: B 776 LYS cc_start: 0.8568 (tttm) cc_final: 0.8280 (tttp) REVERT: B 814 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7870 (mmtt) REVERT: B 868 GLU cc_start: 0.7851 (mp0) cc_final: 0.7430 (mp0) REVERT: B 900 MET cc_start: 0.8521 (mtp) cc_final: 0.8304 (ttm) REVERT: B 902 MET cc_start: 0.8416 (tpp) cc_final: 0.8193 (mmp) REVERT: B 1038 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8134 (mmtm) REVERT: B 1096 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 1116 THR cc_start: 0.8100 (p) cc_final: 0.7758 (t) REVERT: B 1128 VAL cc_start: 0.8735 (p) cc_final: 0.8476 (t) REVERT: C 33 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 41 LYS cc_start: 0.6861 (mmpt) cc_final: 0.5559 (mtpp) REVERT: C 100 ILE cc_start: 0.8591 (tp) cc_final: 0.8363 (pp) REVERT: C 155 SER cc_start: 0.8800 (m) cc_final: 0.8486 (t) REVERT: C 156 GLU cc_start: 0.7294 (pm20) cc_final: 0.6987 (pp20) REVERT: C 189 LEU cc_start: 0.8729 (tt) cc_final: 0.8514 (tp) REVERT: C 304 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8257 (mmtp) REVERT: C 305 SER cc_start: 0.8647 (t) cc_final: 0.8311 (p) REVERT: C 308 VAL cc_start: 0.8718 (t) cc_final: 0.8464 (p) REVERT: C 578 ASP cc_start: 0.7889 (t0) cc_final: 0.7526 (t70) REVERT: C 580 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: C 581 THR cc_start: 0.8102 (m) cc_final: 0.7515 (t) REVERT: C 583 GLU cc_start: 0.7702 (pm20) cc_final: 0.7379 (pm20) REVERT: C 606 ASN cc_start: 0.8935 (m-40) cc_final: 0.8702 (m-40) REVERT: C 651 ILE cc_start: 0.8372 (pt) cc_final: 0.8148 (mt) REVERT: C 661 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 776 LYS cc_start: 0.8516 (tttm) cc_final: 0.8263 (ttmm) REVERT: C 825 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8497 (mtpt) REVERT: C 900 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7982 (mtt) REVERT: C 904 TYR cc_start: 0.7011 (m-10) cc_final: 0.6796 (m-10) REVERT: C 918 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: C 1031 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 1073 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8195 (mmmm) outliers start: 71 outliers final: 54 residues processed: 579 average time/residue: 1.2814 time to fit residues: 859.3129 Evaluate side-chains 605 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 542 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 50 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 266 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 206 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 196 ASN B 239 GLN B 710 ASN B 755 GLN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN C1036 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128091 restraints weight = 35881.693| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.42 r_work: 0.3498 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25108 Z= 0.171 Angle : 0.634 11.913 34254 Z= 0.321 Chirality : 0.047 0.369 3984 Planarity : 0.004 0.042 4356 Dihedral : 5.401 59.143 4080 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.54 % Allowed : 20.81 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3014 helix: 2.36 (0.20), residues: 654 sheet: 0.57 (0.19), residues: 684 loop : -0.87 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 436 HIS 0.003 0.001 HIS A 66 PHE 0.034 0.002 PHE C 592 TYR 0.030 0.001 TYR B 170 ARG 0.007 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 38) link_NAG-ASN : angle 2.99249 ( 114) hydrogen bonds : bond 0.04543 ( 1020) hydrogen bonds : angle 5.35335 ( 2895) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.86216 ( 72) covalent geometry : bond 0.00405 (25034) covalent geometry : angle 0.60585 (34068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24549.65 seconds wall clock time: 427 minutes 23.83 seconds (25643.83 seconds total)