Starting phenix.real_space_refine on Sat May 24 13:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu9_29456/05_2025/8fu9_29456_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 114 5.16 5 C 16091 2.51 5 N 4185 2.21 5 O 4923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25313 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8265 Classifications: {'peptide': 1058} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "B" Number of atoms: 8262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'CIS': 5, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "C" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8254 Classifications: {'peptide': 1056} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 995} Chain breaks: 3 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" 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: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.35, per 1000 atoms: 0.61 Number of scatterers: 25313 At special positions: 0 Unit cell: (143.971, 179.755, 160.615, 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 114 16.00 O 4923 8.00 N 4185 7.00 C 16091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 A1201 " - " ASN A 109 " " NAG A1202 " - " ASN A 262 " " NAG A1203 " - " ASN A 689 " " NAG A1204 " - " ASN A 697 " " NAG A1205 " - " ASN A 781 " " NAG A1206 " - " ASN A1054 " " NAG A1207 " - " ASN A1078 " " NAG A1208 " - " ASN A1114 " " NAG A1209 " - " ASN A 637 " " NAG A1210 " - " ASN A 583 " " NAG A1211 " - " ASN A 61 " " NAG A1212 " - " ASN A 596 " " NAG A1213 " - " ASN A 311 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 262 " " NAG B1203 " - " ASN B 596 " " NAG B1204 " - " ASN B 689 " " NAG B1205 " - " ASN B1054 " " NAG B1206 " - " ASN B 697 " " NAG B1207 " - " ASN B1078 " " NAG B1208 " - " ASN B1114 " " NAG B1209 " - " ASN B 637 " " NAG B1210 " - " ASN B 781 " " NAG B1211 " - " ASN B 583 " " NAG B1212 " - " ASN B 311 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 262 " " NAG C1203 " - " ASN C 596 " " NAG C1204 " - " ASN C 689 " " NAG C1205 " - " ASN C 697 " " NAG C1206 " - " ASN C 781 " " NAG C1207 " - " ASN C1054 " " NAG C1208 " - " ASN C1114 " " NAG C1209 " - " ASN C 323 " " NAG C1210 " - " ASN C 637 " " NAG C1211 " - " ASN C1078 " " NAG C1212 " - " ASN C 583 " " NAG C1213 " - " ASN C 311 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.2 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 23.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.338A pdb=" N LYS A 424 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 726 through 734 removed outlier: 4.229A pdb=" N LEU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 763 removed outlier: 3.787A pdb=" N ASP A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 846 through 864 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 899 through 919 Processing helix chain 'A' and resid 921 through 924 Processing helix chain 'A' and resid 925 through 945 removed outlier: 4.015A pdb=" N VAL A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 948 No H-bonds generated for 'chain 'A' and resid 946 through 948' Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 965 through 1013 removed outlier: 4.857A pdb=" N VAL A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1126 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 717 through 723 Processing helix chain 'B' and resid 726 through 734 Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 738 through 762 removed outlier: 3.971A pdb=" N ASP B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 846 through 865 Processing helix chain 'B' and resid 866 through 870 Processing helix chain 'B' and resid 877 through 888 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.299A pdb=" N LEU B 896 " --> pdb=" O THR B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 920 removed outlier: 3.695A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 915 " --> pdb=" O ILE B 911 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 916 " --> pdb=" O GLY B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 945 Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 965 through 1013 removed outlier: 3.737A pdb=" N GLN B 972 " --> pdb=" O GLU B 968 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 726 through 734 Processing helix chain 'C' and resid 735 through 737 No H-bonds generated for 'chain 'C' and resid 735 through 737' Processing helix chain 'C' and resid 738 through 763 removed outlier: 4.099A pdb=" N ASN C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 866 through 870 Processing helix chain 'C' and resid 877 through 888 Processing helix chain 'C' and resid 892 through 899 removed outlier: 4.387A pdb=" N LEU C 896 " --> pdb=" O THR C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 913 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 921 through 924 Processing helix chain 'C' and resid 925 through 945 removed outlier: 3.862A pdb=" N VAL C 931 " --> pdb=" O LYS C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 964 Processing helix chain 'C' and resid 965 through 1013 removed outlier: 4.330A pdb=" N VAL C 971 " --> pdb=" O PRO C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1125 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.754A pdb=" N HIS A 194 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ALA A 209 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N PHE A 207 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.500A pdb=" N VAL A 47 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 267 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 299 removed outlier: 5.341A pdb=" N ILE A 292 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 579 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN A 294 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 577 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A 574 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 308 removed outlier: 6.160A pdb=" N GLU A 304 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASN A 522 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 306 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.964A pdb=" N VAL A 375 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN A 374 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 496 " --> pdb=" O ASN A 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.690A pdb=" N CYS A 341 " --> pdb=" O CYS A 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA9, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.620A pdb=" N ILE A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 684 removed outlier: 6.698A pdb=" N ALA A 681 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS B 770 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN A 683 " --> pdb=" O LYS B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.442A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER A1035 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1041 " --> pdb=" O PRO A1033 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A1043 " --> pdb=" O SER A1031 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A1031 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A1045 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.442A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A1058 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A1075 " --> pdb=" O ALA A1058 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 716 removed outlier: 4.238A pdb=" N LYS A 713 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 767 through 770 Processing sheet with id=AB6, first strand: chain 'A' and resid 1100 through 1102 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.902A pdb=" N ILE B 190 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.581A pdb=" N ASP B 267 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 93 removed outlier: 4.462A pdb=" N GLY B 90 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 228 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 299 removed outlier: 5.278A pdb=" N ILE B 292 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 579 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLN B 294 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 577 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 296 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY B 574 " --> pdb=" O GLN B 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 334 through 338 Processing sheet with id=AC3, first strand: chain 'B' and resid 341 through 342 removed outlier: 6.808A pdb=" N CYS B 341 " --> pdb=" O CYS B 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 518 through 523 removed outlier: 5.442A pdb=" N ASP B 554 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 555 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE B 545 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 634 through 640 removed outlier: 5.158A pdb=" N THR B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 638 " --> pdb=" O THR B 676 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 681 through 684 removed outlier: 6.861A pdb=" N ALA B 681 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS C 770 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN B 683 " --> pdb=" O LYS C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.595A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B1047 " --> pdb=" O HIS B1028 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS B1028 " --> pdb=" O TYR B1047 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.595A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B1086 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B1091 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 713 through 716 removed outlier: 4.267A pdb=" N LYS B 713 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1100 through 1105 removed outlier: 4.863A pdb=" N ALA B1067 " --> pdb=" O SER B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.723A pdb=" N GLU C 211 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N HIS C 194 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N ALA C 209 " --> pdb=" O HIS C 194 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 36 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.826A pdb=" N THR C 254 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP C 270 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 256 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA C 268 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 258 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AD5, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AD6, first strand: chain 'C' and resid 291 through 299 removed outlier: 5.224A pdb=" N ILE C 292 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR C 579 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN C 294 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 577 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 574 " --> pdb=" O GLN C 593 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 304 through 308 removed outlier: 4.417A pdb=" N GLU C 304 " --> pdb=" O CYS C 518 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 334 through 338 removed outlier: 4.068A pdb=" N VAL C 375 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN C 374 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 496 " --> pdb=" O ASN C 374 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 342 removed outlier: 6.476A pdb=" N CYS C 341 " --> pdb=" O CYS C 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.764A pdb=" N ILE C 650 " --> pdb=" O ILE C 646 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.417A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C1047 " --> pdb=" O HIS C1028 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N HIS C1028 " --> pdb=" O TYR C1047 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.417A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C1058 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE C1075 " --> pdb=" O ALA C1058 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 713 through 716 removed outlier: 4.208A pdb=" N LYS C 713 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1100 through 1105 removed outlier: 5.599A pdb=" N ALA C1067 " --> pdb=" O SER C1103 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2553 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: 10.05 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4526 1.32 - 1.44: 6776 1.44 - 1.57: 14400 1.57 - 1.70: 36 1.70 - 1.82: 145 Bond restraints: 25883 Sorted by residual: bond pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " ideal model delta sigma weight residual 1.516 1.726 -0.210 2.50e-02 1.60e+03 7.06e+01 bond pdb=" N PRO C 487 " pdb=" CA PRO C 487 " ideal model delta sigma weight residual 1.473 1.442 0.031 8.50e-03 1.38e+04 1.33e+01 bond pdb=" CB ASN C 894 " pdb=" CG ASN C 894 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.27e+01 bond pdb=" CB LEU B 808 " pdb=" CG LEU B 808 " ideal model delta sigma weight residual 1.530 1.598 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB LEU B1125 " pdb=" CG LEU B1125 " ideal model delta sigma weight residual 1.530 1.596 -0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 25878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.21: 35216 9.21 - 18.42: 6 18.42 - 27.64: 0 27.64 - 36.85: 1 36.85 - 46.06: 1 Bond angle restraints: 35224 Sorted by residual: angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" OD1 ASN A 689 " ideal model delta sigma weight residual 120.80 74.74 46.06 2.00e+00 2.50e-01 5.30e+02 angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 116.40 85.25 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" OD1 ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 122.60 131.81 -9.21 1.00e+00 1.00e+00 8.48e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.23 -6.57 7.20e-01 1.93e+00 8.34e+01 angle pdb=" C GLU A 211 " pdb=" N PRO A 212 " pdb=" CA PRO A 212 " ideal model delta sigma weight residual 119.85 128.39 -8.54 1.01e+00 9.80e-01 7.15e+01 ... (remaining 35219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15229 17.71 - 35.42: 434 35.42 - 53.13: 98 53.13 - 70.85: 61 70.85 - 88.56: 28 Dihedral angle restraints: 15850 sinusoidal: 6615 harmonic: 9235 Sorted by residual: dihedral pdb=" CA THR B 921 " pdb=" C THR B 921 " pdb=" N PRO B 922 " pdb=" CA PRO B 922 " ideal model delta harmonic sigma weight residual -180.00 -143.46 -36.54 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ASP B1119 " pdb=" C ASP B1119 " pdb=" N PRO B1120 " pdb=" CA PRO B1120 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N ILE A 106 " pdb=" CA ILE A 106 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 15847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3122 0.079 - 0.157: 766 0.157 - 0.236: 146 0.236 - 0.314: 39 0.314 - 0.393: 21 Chirality restraints: 4094 Sorted by residual: chirality pdb=" C2 NAG B1201 " pdb=" C1 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" N2 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2 NAG B1203 " pdb=" C1 NAG B1203 " pdb=" C3 NAG B1203 " pdb=" N2 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1 NAG A1213 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG A1213 " pdb=" O5 NAG A1213 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4091 not shown) Planarity restraints: 4573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 pdb=" C1 NAG A1203 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 2.06e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 596 " 0.048 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" CG ASN B 596 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 596 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 596 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1203 " 0.058 2.00e-02 2.50e+03 ... (remaining 4570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5455 2.77 - 3.30: 23088 3.30 - 3.84: 40859 3.84 - 4.37: 48951 4.37 - 4.90: 81155 Nonbonded interactions: 199508 Sorted by model distance: nonbonded pdb=" OG1 THR C 33 " pdb=" O PRO C 204 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.280 3.040 nonbonded pdb=" N ASN A 689 " pdb=" OD1 ASN A 689 " model vdw 2.333 3.120 nonbonded pdb=" OG SER C 864 " pdb=" OG1 THR C 867 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A1103 " pdb=" N GLY A1104 " model vdw 2.353 3.120 ... (remaining 199503 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 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) selection = (chain 'B' and (resid 14 through 807 or resid 834 through 1125 or resid 1201 thr \ ough 1212)) selection = (chain 'C' and (resid 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 56.020 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.012 0.210 25921 Z= 0.655 Angle : 1.353 46.062 35338 Z= 0.896 Chirality : 0.077 0.393 4094 Planarity : 0.006 0.206 4535 Dihedral : 10.901 88.557 9912 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.45 % Favored : 93.07 % Rotamer: Outliers : 0.14 % Allowed : 0.65 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.62 % 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: -0.76 (0.14), residues: 3147 helix: 0.52 (0.19), residues: 624 sheet: 0.64 (0.21), residues: 560 loop : -1.26 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP A 866 HIS 0.005 0.001 HIS C 499 PHE 0.025 0.003 PHE B 122 TYR 0.035 0.004 TYR C 187 ARG 0.003 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.06241 ( 38) link_NAG-ASN : angle 2.47117 ( 114) hydrogen bonds : bond 0.17575 ( 903) hydrogen bonds : angle 7.96280 ( 2553) covalent geometry : bond 0.01185 (25883) covalent geometry : angle 1.34818 (35224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 2.834 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 79 PHE cc_start: 0.4536 (m-80) cc_final: 0.2844 (m-80) REVERT: A 164 MET cc_start: 0.5980 (tpt) cc_final: 0.4901 (mmm) REVERT: A 176 LEU cc_start: 0.7641 (pp) cc_final: 0.7426 (pp) REVERT: A 544 GLN cc_start: 0.6350 (mm-40) cc_final: 0.5957 (mm110) REVERT: A 572 PHE cc_start: 0.7997 (p90) cc_final: 0.7759 (p90) REVERT: A 634 GLU cc_start: 0.8209 (tt0) cc_final: 0.7983 (tt0) REVERT: A 717 ASP cc_start: 0.7926 (t0) cc_final: 0.7720 (t0) REVERT: A 848 GLU cc_start: 0.8186 (mp0) cc_final: 0.7923 (mm-30) REVERT: B 79 PHE cc_start: 0.4919 (m-80) cc_final: 0.4374 (m-80) REVERT: B 179 PHE cc_start: 0.8205 (m-80) cc_final: 0.7952 (m-10) REVERT: B 187 TYR cc_start: 0.7370 (m-80) cc_final: 0.7068 (m-80) REVERT: B 249 TYR cc_start: 0.7436 (m-80) cc_final: 0.6971 (m-80) REVERT: B 517 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7061 (tptt) REVERT: B 552 THR cc_start: 0.7674 (p) cc_final: 0.7236 (m) REVERT: B 1116 THR cc_start: 0.8589 (m) cc_final: 0.8383 (p) REVERT: B 1118 TYR cc_start: 0.7152 (m-80) cc_final: 0.6838 (m-80) REVERT: C 193 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7782 (mmmt) REVERT: C 288 VAL cc_start: 0.8697 (t) cc_final: 0.8280 (t) REVERT: C 293 TYR cc_start: 0.8660 (m-80) cc_final: 0.8063 (m-80) REVERT: C 296 SER cc_start: 0.8309 (t) cc_final: 0.7754 (m) REVERT: C 297 ASN cc_start: 0.8550 (m-40) cc_final: 0.8109 (m-40) REVERT: C 333 TRP cc_start: 0.6253 (p90) cc_final: 0.5763 (p90) REVERT: C 369 ASP cc_start: 0.7792 (m-30) cc_final: 0.7451 (m-30) REVERT: C 432 GLN cc_start: 0.5805 (mt0) cc_final: 0.5401 (mp10) REVERT: C 754 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8612 (mp10) REVERT: C 836 ASN cc_start: 0.6947 (m-40) cc_final: 0.6690 (m110) REVERT: C 947 SER cc_start: 0.8700 (m) cc_final: 0.8475 (p) REVERT: C 985 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8291 (tp40) outliers start: 4 outliers final: 2 residues processed: 541 average time/residue: 0.4012 time to fit residues: 331.4491 Evaluate side-chains 256 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain C residue 1054 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.1980 chunk 183 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 HIS A 935 ASN A 990 GLN A1038 HIS B 670 GLN B 836 ASN B 937 GLN C 205 GLN C 594 ASN C 990 GLN C1081 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119610 restraints weight = 41084.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122428 restraints weight = 25599.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121666 restraints weight = 17272.396| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25921 Z= 0.155 Angle : 0.734 13.437 35338 Z= 0.386 Chirality : 0.049 0.285 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.924 58.865 4204 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 5.97 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -0.62 (0.15), residues: 3147 helix: 1.64 (0.21), residues: 624 sheet: 0.20 (0.20), residues: 637 loop : -1.42 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 866 HIS 0.012 0.001 HIS B 49 PHE 0.032 0.002 PHE C 380 TYR 0.022 0.002 TYR B1047 ARG 0.006 0.000 ARG A 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 38) link_NAG-ASN : angle 3.33246 ( 114) hydrogen bonds : bond 0.05368 ( 903) hydrogen bonds : angle 6.16223 ( 2553) covalent geometry : bond 0.00331 (25883) covalent geometry : angle 0.71034 (35224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 2.485 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 113 VAL cc_start: 0.7120 (p) cc_final: 0.6810 (p) REVERT: A 164 MET cc_start: 0.5744 (tpt) cc_final: 0.5420 (mmm) REVERT: A 176 LEU cc_start: 0.7488 (pp) cc_final: 0.6988 (pp) REVERT: A 178 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6760 (mp0) REVERT: A 181 PHE cc_start: 0.6492 (t80) cc_final: 0.5988 (t80) REVERT: A 371 CYS cc_start: 0.8165 (m) cc_final: 0.7867 (m) REVERT: B 179 PHE cc_start: 0.7954 (m-80) cc_final: 0.7565 (m-80) REVERT: B 249 TYR cc_start: 0.7231 (m-80) cc_final: 0.6681 (m-80) REVERT: B 547 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7032 (mmm-85) REVERT: B 836 ASN cc_start: 0.8132 (m110) cc_final: 0.7854 (m110) REVERT: B 849 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7321 (mtm) REVERT: C 269 VAL cc_start: 0.8763 (t) cc_final: 0.8519 (m) REVERT: C 296 SER cc_start: 0.8185 (t) cc_final: 0.7821 (m) REVERT: C 297 ASN cc_start: 0.8276 (m-40) cc_final: 0.8030 (m-40) REVERT: C 333 TRP cc_start: 0.5738 (p90) cc_final: 0.5261 (p90) REVERT: C 369 ASP cc_start: 0.7470 (m-30) cc_final: 0.7138 (m-30) REVERT: C 380 PHE cc_start: 0.6634 (m-80) cc_final: 0.6405 (m-80) REVERT: C 432 GLN cc_start: 0.6165 (mt0) cc_final: 0.5960 (mp10) REVERT: C 947 SER cc_start: 0.8305 (m) cc_final: 0.7977 (p) outliers start: 43 outliers final: 24 residues processed: 323 average time/residue: 0.3599 time to fit residues: 182.3760 Evaluate side-chains 236 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 226 GLN B 935 ASN C 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.180282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118323 restraints weight = 41236.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118268 restraints weight = 25774.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118884 restraints weight = 22108.710| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25921 Z= 0.147 Angle : 0.668 13.033 35338 Z= 0.348 Chirality : 0.047 0.305 4094 Planarity : 0.004 0.076 4535 Dihedral : 5.714 58.599 4202 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.45 % Rotamer: Outliers : 1.48 % Allowed : 8.46 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3147 helix: 1.73 (0.21), residues: 626 sheet: 0.01 (0.20), residues: 620 loop : -1.42 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 139 HIS 0.006 0.001 HIS B 49 PHE 0.030 0.002 PHE C 380 TYR 0.022 0.001 TYR B1047 ARG 0.016 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 38) link_NAG-ASN : angle 3.09289 ( 114) hydrogen bonds : bond 0.04885 ( 903) hydrogen bonds : angle 5.77018 ( 2553) covalent geometry : bond 0.00322 (25883) covalent geometry : angle 0.64521 (35224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 2.594 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 113 VAL cc_start: 0.7071 (p) cc_final: 0.6739 (p) REVERT: A 164 MET cc_start: 0.5867 (tpt) cc_final: 0.5247 (mmm) REVERT: A 176 LEU cc_start: 0.7340 (pp) cc_final: 0.6763 (pp) REVERT: A 178 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6733 (mp0) REVERT: A 181 PHE cc_start: 0.6542 (t80) cc_final: 0.5979 (t80) REVERT: A 371 CYS cc_start: 0.8087 (m) cc_final: 0.7780 (m) REVERT: A 544 GLN cc_start: 0.6352 (mm-40) cc_final: 0.5990 (pt0) REVERT: A 682 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 179 PHE cc_start: 0.7925 (m-80) cc_final: 0.7627 (m-80) REVERT: B 193 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7388 (ttmm) REVERT: B 249 TYR cc_start: 0.7221 (m-80) cc_final: 0.6616 (m-80) REVERT: B 547 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.6853 (mmm-85) REVERT: B 836 ASN cc_start: 0.8113 (m110) cc_final: 0.7854 (m110) REVERT: B 929 GLN cc_start: 0.8356 (tp40) cc_final: 0.8102 (mm-40) REVERT: C 187 TYR cc_start: 0.7092 (t80) cc_final: 0.6778 (t80) REVERT: C 250 LEU cc_start: 0.7424 (mp) cc_final: 0.7119 (mp) REVERT: C 269 VAL cc_start: 0.8715 (t) cc_final: 0.8498 (m) REVERT: C 296 SER cc_start: 0.8172 (t) cc_final: 0.7828 (m) REVERT: C 297 ASN cc_start: 0.8296 (m-40) cc_final: 0.7976 (m-40) REVERT: C 333 TRP cc_start: 0.5467 (p90) cc_final: 0.5099 (p90) REVERT: C 369 ASP cc_start: 0.7506 (m-30) cc_final: 0.7183 (m-30) REVERT: C 380 PHE cc_start: 0.6559 (m-80) cc_final: 0.6305 (m-10) REVERT: C 432 GLN cc_start: 0.6018 (mt0) cc_final: 0.5734 (mp10) REVERT: C 947 SER cc_start: 0.8391 (m) cc_final: 0.8012 (p) outliers start: 41 outliers final: 27 residues processed: 280 average time/residue: 0.3419 time to fit residues: 155.2349 Evaluate side-chains 232 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 311 optimal weight: 0.9990 chunk 313 optimal weight: 0.0570 chunk 21 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN B 49 HIS B 205 GLN B 881 GLN ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 544 GLN C 635 HIS C 894 ASN C 982 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.173463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113537 restraints weight = 42091.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111540 restraints weight = 24953.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111888 restraints weight = 18294.881| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 25921 Z= 0.242 Angle : 0.735 12.249 35338 Z= 0.380 Chirality : 0.050 0.319 4094 Planarity : 0.005 0.062 4535 Dihedral : 6.157 56.933 4202 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 2.02 % Allowed : 8.96 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3147 helix: 1.37 (0.21), residues: 628 sheet: -0.26 (0.20), residues: 603 loop : -1.69 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 866 HIS 0.006 0.001 HIS C 635 PHE 0.028 0.002 PHE B 225 TYR 0.029 0.002 TYR B1047 ARG 0.007 0.001 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 38) link_NAG-ASN : angle 3.22213 ( 114) hydrogen bonds : bond 0.05178 ( 903) hydrogen bonds : angle 5.85623 ( 2553) covalent geometry : bond 0.00573 (25883) covalent geometry : angle 0.71302 (35224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5704 (tpt) cc_final: 0.5126 (mmm) REVERT: A 176 LEU cc_start: 0.7392 (pp) cc_final: 0.7049 (pp) REVERT: A 178 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6537 (mp0) REVERT: A 371 CYS cc_start: 0.8055 (m) cc_final: 0.7772 (m) REVERT: B 193 LYS cc_start: 0.7614 (ttpp) cc_final: 0.7350 (ttmm) REVERT: B 249 TYR cc_start: 0.7117 (m-80) cc_final: 0.6450 (m-80) REVERT: B 547 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7301 (mmm-85) REVERT: B 836 ASN cc_start: 0.8161 (m110) cc_final: 0.7885 (m110) REVERT: B 929 GLN cc_start: 0.8449 (tp40) cc_final: 0.8181 (mm-40) REVERT: B 963 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7800 (ttm170) REVERT: C 41 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7296 (mmtm) REVERT: C 192 SER cc_start: 0.8385 (p) cc_final: 0.8131 (t) REVERT: C 210 LEU cc_start: 0.7830 (mt) cc_final: 0.7532 (mm) REVERT: C 269 VAL cc_start: 0.8715 (t) cc_final: 0.8511 (m) REVERT: C 296 SER cc_start: 0.8194 (t) cc_final: 0.7870 (m) REVERT: C 333 TRP cc_start: 0.5472 (p90) cc_final: 0.5158 (p90) REVERT: C 369 ASP cc_start: 0.7570 (m-30) cc_final: 0.7250 (m-30) REVERT: C 432 GLN cc_start: 0.6117 (mt0) cc_final: 0.5872 (mp10) REVERT: C 513 LEU cc_start: 0.8344 (mt) cc_final: 0.8072 (mp) REVERT: C 720 MET cc_start: 0.7190 (ttt) cc_final: 0.6920 (tpt) REVERT: C 947 SER cc_start: 0.8598 (m) cc_final: 0.8215 (p) outliers start: 56 outliers final: 41 residues processed: 269 average time/residue: 0.3459 time to fit residues: 149.2503 Evaluate side-chains 232 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 953 ILE Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1085 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 162 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 251 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 49 HIS B1063 HIS C 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116736 restraints weight = 41976.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115436 restraints weight = 26646.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115092 restraints weight = 20280.363| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25921 Z= 0.126 Angle : 0.643 12.769 35338 Z= 0.331 Chirality : 0.047 0.321 4094 Planarity : 0.004 0.059 4535 Dihedral : 5.738 57.929 4202 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.45 % Rotamer: Outliers : 1.84 % Allowed : 10.08 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -0.91 (0.15), residues: 3147 helix: 1.81 (0.21), residues: 621 sheet: -0.37 (0.19), residues: 638 loop : -1.61 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 416 HIS 0.008 0.001 HIS C 499 PHE 0.023 0.001 PHE C 521 TYR 0.018 0.001 TYR A1047 ARG 0.008 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 38) link_NAG-ASN : angle 2.92502 ( 114) hydrogen bonds : bond 0.04351 ( 903) hydrogen bonds : angle 5.52902 ( 2553) covalent geometry : bond 0.00266 (25883) covalent geometry : angle 0.62173 (35224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5782 (tpt) cc_final: 0.5178 (mmm) REVERT: A 176 LEU cc_start: 0.7368 (pp) cc_final: 0.7024 (pp) REVERT: A 178 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6561 (mp0) REVERT: A 380 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.4738 (m-80) REVERT: A 544 GLN cc_start: 0.6473 (mm-40) cc_final: 0.6153 (pt0) REVERT: B 193 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7304 (ttmm) REVERT: B 249 TYR cc_start: 0.7212 (m-80) cc_final: 0.6557 (m-80) REVERT: B 547 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7144 (mmm-85) REVERT: B 551 ASP cc_start: 0.7509 (t0) cc_final: 0.7206 (t0) REVERT: B 836 ASN cc_start: 0.8149 (m110) cc_final: 0.7869 (m110) REVERT: B 963 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7660 (ttm170) REVERT: C 192 SER cc_start: 0.8377 (p) cc_final: 0.8100 (t) REVERT: C 210 LEU cc_start: 0.7777 (mt) cc_final: 0.7535 (mm) REVERT: C 369 ASP cc_start: 0.7510 (m-30) cc_final: 0.7199 (m-30) REVERT: C 720 MET cc_start: 0.7052 (ttt) cc_final: 0.6810 (tpt) REVERT: C 970 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7838 (tt0) outliers start: 51 outliers final: 36 residues processed: 258 average time/residue: 0.3827 time to fit residues: 163.0745 Evaluate side-chains 234 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1084 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 28 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 166 optimal weight: 0.2980 chunk 181 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 234 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS C 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117035 restraints weight = 41789.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115909 restraints weight = 25599.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115496 restraints weight = 19569.599| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 25921 Z= 0.129 Angle : 0.637 12.521 35338 Z= 0.327 Chirality : 0.046 0.320 4094 Planarity : 0.004 0.047 4535 Dihedral : 5.651 58.425 4202 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 2.05 % Allowed : 10.47 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -0.91 (0.15), residues: 3147 helix: 1.89 (0.21), residues: 620 sheet: -0.44 (0.19), residues: 633 loop : -1.60 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 416 HIS 0.002 0.001 HIS C 194 PHE 0.029 0.001 PHE A 181 TYR 0.021 0.001 TYR C 403 ARG 0.006 0.000 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 38) link_NAG-ASN : angle 2.84056 ( 114) hydrogen bonds : bond 0.04213 ( 903) hydrogen bonds : angle 5.43114 ( 2553) covalent geometry : bond 0.00283 (25883) covalent geometry : angle 0.61679 (35224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6822 (tp) REVERT: A 164 MET cc_start: 0.5773 (tpt) cc_final: 0.5112 (mmm) REVERT: A 178 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6500 (mp0) REVERT: A 371 CYS cc_start: 0.7904 (m) cc_final: 0.7610 (m) REVERT: A 380 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4724 (m-80) REVERT: A 544 GLN cc_start: 0.6506 (mm-40) cc_final: 0.6187 (pt0) REVERT: B 179 PHE cc_start: 0.7940 (m-80) cc_final: 0.7363 (m-80) REVERT: B 249 TYR cc_start: 0.7172 (m-80) cc_final: 0.6582 (m-80) REVERT: B 544 GLN cc_start: 0.7944 (mp10) cc_final: 0.7728 (mp10) REVERT: B 547 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7071 (mmm-85) REVERT: B 836 ASN cc_start: 0.8157 (m110) cc_final: 0.7882 (m110) REVERT: C 369 ASP cc_start: 0.7476 (m-30) cc_final: 0.7174 (m-30) REVERT: C 473 GLN cc_start: 0.6641 (mm-40) cc_final: 0.5796 (mt0) REVERT: C 970 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7804 (tt0) outliers start: 57 outliers final: 39 residues processed: 249 average time/residue: 0.3304 time to fit residues: 135.4727 Evaluate side-chains 227 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121476 restraints weight = 42042.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121042 restraints weight = 38183.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113874 restraints weight = 23292.087| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25921 Z= 0.202 Angle : 0.682 12.535 35338 Z= 0.349 Chirality : 0.048 0.325 4094 Planarity : 0.004 0.049 4535 Dihedral : 5.916 58.969 4202 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 2.63 % Allowed : 10.47 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3147 helix: 1.72 (0.21), residues: 620 sheet: -0.72 (0.19), residues: 624 loop : -1.71 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 416 HIS 0.005 0.001 HIS C 499 PHE 0.037 0.002 PHE C 521 TYR 0.026 0.002 TYR B1047 ARG 0.006 0.001 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 38) link_NAG-ASN : angle 3.01305 ( 114) hydrogen bonds : bond 0.04625 ( 903) hydrogen bonds : angle 5.55570 ( 2553) covalent geometry : bond 0.00478 (25883) covalent geometry : angle 0.66146 (35224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5481 (tpt) cc_final: 0.4892 (mmm) REVERT: A 178 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6697 (mp0) REVERT: A 337 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.7173 (mmp-170) REVERT: A 371 CYS cc_start: 0.7904 (m) cc_final: 0.7569 (m) REVERT: A 380 PHE cc_start: 0.4946 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: A 490 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6426 (m) REVERT: B 249 TYR cc_start: 0.7100 (m-80) cc_final: 0.6730 (m-80) REVERT: B 547 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: B 836 ASN cc_start: 0.8169 (m110) cc_final: 0.7888 (m110) REVERT: B 963 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7767 (ttm170) REVERT: C 369 ASP cc_start: 0.7438 (m-30) cc_final: 0.7141 (m-30) REVERT: C 473 GLN cc_start: 0.6038 (mm-40) cc_final: 0.5769 (mt0) outliers start: 73 outliers final: 50 residues processed: 250 average time/residue: 0.3283 time to fit residues: 136.2121 Evaluate side-chains 239 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1085 THR Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122996 restraints weight = 41932.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121687 restraints weight = 37895.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122587 restraints weight = 27519.018| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25921 Z= 0.128 Angle : 0.633 12.230 35338 Z= 0.325 Chirality : 0.046 0.321 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.685 58.042 4202 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.51 % Favored : 93.39 % Rotamer: Outliers : 2.16 % Allowed : 11.08 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3147 helix: 1.89 (0.21), residues: 620 sheet: -0.58 (0.20), residues: 601 loop : -1.71 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 416 HIS 0.003 0.000 HIS C 194 PHE 0.030 0.001 PHE C 521 TYR 0.019 0.001 TYR C 403 ARG 0.006 0.000 ARG C 975 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 38) link_NAG-ASN : angle 2.80825 ( 114) hydrogen bonds : bond 0.04169 ( 903) hydrogen bonds : angle 5.37284 ( 2553) covalent geometry : bond 0.00279 (25883) covalent geometry : angle 0.61337 (35224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5537 (tpt) cc_final: 0.4924 (mmm) REVERT: A 371 CYS cc_start: 0.7704 (m) cc_final: 0.7370 (m) REVERT: A 490 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6431 (m) REVERT: B 836 ASN cc_start: 0.8049 (m110) cc_final: 0.7819 (m110) REVERT: C 369 ASP cc_start: 0.7145 (m-30) cc_final: 0.6881 (m-30) REVERT: C 970 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7650 (tt0) outliers start: 60 outliers final: 48 residues processed: 248 average time/residue: 0.3207 time to fit residues: 133.5433 Evaluate side-chains 240 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1085 THR Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 182 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS C 194 HIS C 297 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122359 restraints weight = 41976.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122182 restraints weight = 36403.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121390 restraints weight = 23545.398| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25921 Z= 0.135 Angle : 0.637 12.357 35338 Z= 0.326 Chirality : 0.046 0.322 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.648 58.589 4202 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 2.02 % Allowed : 11.26 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3147 helix: 1.94 (0.21), residues: 619 sheet: -0.58 (0.20), residues: 610 loop : -1.73 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 416 HIS 0.003 0.001 HIS C 194 PHE 0.034 0.001 PHE B 225 TYR 0.020 0.001 TYR B1047 ARG 0.011 0.000 ARG B 547 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 38) link_NAG-ASN : angle 2.80575 ( 114) hydrogen bonds : bond 0.04110 ( 903) hydrogen bonds : angle 5.31041 ( 2553) covalent geometry : bond 0.00303 (25883) covalent geometry : angle 0.61806 (35224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5421 (tpt) cc_final: 0.4804 (mmm) REVERT: A 371 CYS cc_start: 0.7691 (m) cc_final: 0.7438 (t) REVERT: B 836 ASN cc_start: 0.8076 (m110) cc_final: 0.7831 (m110) REVERT: C 369 ASP cc_start: 0.7167 (m-30) cc_final: 0.6902 (m-30) REVERT: C 970 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7613 (tt0) outliers start: 56 outliers final: 50 residues processed: 242 average time/residue: 0.3309 time to fit residues: 134.7367 Evaluate side-chains 244 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 711 MET Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1085 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 136 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 49 HIS ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C1068 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.171475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117362 restraints weight = 41958.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114284 restraints weight = 43263.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115827 restraints weight = 34264.521| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 25921 Z= 0.294 Angle : 0.774 12.283 35338 Z= 0.395 Chirality : 0.051 0.335 4094 Planarity : 0.005 0.043 4535 Dihedral : 6.421 55.746 4202 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 2.05 % Allowed : 11.16 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3147 helix: 1.34 (0.21), residues: 627 sheet: -0.88 (0.20), residues: 617 loop : -2.01 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 416 HIS 0.009 0.001 HIS C1028 PHE 0.027 0.002 PHE C 521 TYR 0.033 0.002 TYR B1047 ARG 0.008 0.001 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 38) link_NAG-ASN : angle 3.30923 ( 114) hydrogen bonds : bond 0.05178 ( 903) hydrogen bonds : angle 5.81603 ( 2553) covalent geometry : bond 0.00704 (25883) covalent geometry : angle 0.75158 (35224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 836 ASN cc_start: 0.8099 (m110) cc_final: 0.7865 (m110) REVERT: C 58 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6257 (m-10) REVERT: C 369 ASP cc_start: 0.7487 (m-30) cc_final: 0.7166 (m-30) REVERT: C 473 GLN cc_start: 0.4434 (mt0) cc_final: 0.3744 (tm-30) outliers start: 57 outliers final: 47 residues processed: 235 average time/residue: 0.3424 time to fit residues: 131.8746 Evaluate side-chains 231 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 894 ASN Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1085 THR Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 171 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.174518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122572 restraints weight = 41741.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122056 restraints weight = 39904.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119051 restraints weight = 25058.868| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25921 Z= 0.135 Angle : 0.659 12.106 35338 Z= 0.336 Chirality : 0.047 0.321 4094 Planarity : 0.004 0.043 4535 Dihedral : 5.920 58.493 4202 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.80 % Favored : 93.10 % Rotamer: Outliers : 1.48 % Allowed : 11.80 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3147 helix: 1.73 (0.21), residues: 619 sheet: -0.79 (0.20), residues: 620 loop : -1.91 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 416 HIS 0.004 0.001 HIS C1068 PHE 0.028 0.001 PHE C 521 TYR 0.023 0.001 TYR C 403 ARG 0.006 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 38) link_NAG-ASN : angle 3.02708 ( 114) hydrogen bonds : bond 0.04255 ( 903) hydrogen bonds : angle 5.43829 ( 2553) covalent geometry : bond 0.00301 (25883) covalent geometry : angle 0.63688 (35224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9346.94 seconds wall clock time: 164 minutes 34.81 seconds (9874.81 seconds total)