Starting phenix.real_space_refine on Mon Aug 25 05:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu9_29456/08_2025/8fu9_29456_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu9_29456/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fu9_29456/08_2025/8fu9_29456_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu9_29456/08_2025/8fu9_29456_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fu9_29456/08_2025/8fu9_29456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu9_29456/08_2025/8fu9_29456.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.21, per 1000 atoms: 0.21 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: 2.07 Conformation dependent library (CDL) restraints added in 863.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.00 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: 4.73 Time building geometry restraints manager: 2.55 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 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- 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 : 2.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG C 437 TYR 0.035 0.004 TYR C 187 PHE 0.025 0.003 PHE B 122 TRP 0.033 0.005 TRP A 866 HIS 0.005 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.01185 (25883) covalent geometry : angle 1.34818 (35224) hydrogen bonds : bond 0.17575 ( 903) hydrogen bonds : angle 7.96280 ( 2553) link_NAG-ASN : bond 0.06241 ( 38) link_NAG-ASN : angle 2.47117 ( 114) *********************** 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 : 0.642 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: 0.2899 (m-80) REVERT: A 164 MET cc_start: 0.5980 (tpt) cc_final: 0.4905 (mmm) REVERT: A 176 LEU cc_start: 0.7641 (pp) cc_final: 0.7153 (pp) REVERT: A 544 GLN cc_start: 0.6350 (mm-40) cc_final: 0.5970 (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: 0.7924 (mm-30) REVERT: B 79 PHE cc_start: 0.4919 (m-80) cc_final: 0.4376 (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: 0.7070 (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: 0.8382 (p) REVERT: B 1118 TYR cc_start: 0.7152 (m-80) cc_final: 0.6837 (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: 0.8064 (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: 0.7458 (m-30) REVERT: C 432 GLN cc_start: 0.5805 (mt0) cc_final: 0.5403 (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: 0.8474 (p) REVERT: C 985 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8289 (tp40) outliers start: 4 outliers final: 2 residues processed: 541 average time/residue: 0.1618 time to fit residues: 135.4595 Evaluate side-chains 254 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 635 HIS A 935 ASN A 990 GLN A1038 HIS B 52 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.182450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122053 restraints weight = 41820.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120840 restraints weight = 25224.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120913 restraints weight = 20864.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121373 restraints weight = 18113.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121677 restraints weight = 16937.115| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25921 Z= 0.185 Angle : 0.748 13.307 35338 Z= 0.395 Chirality : 0.050 0.298 4094 Planarity : 0.005 0.050 4535 Dihedral : 6.002 59.258 4204 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 6.08 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 3147 helix: 1.57 (0.21), residues: 625 sheet: 0.03 (0.19), residues: 652 loop : -1.45 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 337 TYR 0.024 0.002 TYR B1047 PHE 0.029 0.002 PHE C 380 TRP 0.021 0.002 TRP A 866 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00416 (25883) covalent geometry : angle 0.72385 (35224) hydrogen bonds : bond 0.05598 ( 903) hydrogen bonds : angle 6.17006 ( 2553) link_NAG-ASN : bond 0.00507 ( 38) link_NAG-ASN : angle 3.36753 ( 114) *********************** 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 322 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.008 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 113 VAL cc_start: 0.7181 (p) cc_final: 0.6900 (p) REVERT: A 164 MET cc_start: 0.5761 (tpt) cc_final: 0.5318 (mmm) REVERT: A 176 LEU cc_start: 0.7477 (pp) cc_final: 0.7265 (pp) REVERT: A 371 CYS cc_start: 0.8177 (m) cc_final: 0.7864 (m) REVERT: B 179 PHE cc_start: 0.7971 (m-80) cc_final: 0.7561 (m-80) REVERT: B 249 TYR cc_start: 0.7301 (m-80) cc_final: 0.6631 (m-80) REVERT: B 547 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7068 (mmm-85) REVERT: B 836 ASN cc_start: 0.8164 (m110) cc_final: 0.7871 (m110) REVERT: C 269 VAL cc_start: 0.8737 (t) cc_final: 0.8485 (m) REVERT: C 296 SER cc_start: 0.8161 (t) cc_final: 0.7775 (m) REVERT: C 297 ASN cc_start: 0.8335 (m-40) cc_final: 0.8101 (m-40) REVERT: C 333 TRP cc_start: 0.5721 (p90) cc_final: 0.5224 (p90) REVERT: C 369 ASP cc_start: 0.7547 (m-30) cc_final: 0.7198 (m-30) REVERT: C 372 PHE cc_start: 0.8003 (m-80) cc_final: 0.7725 (m-80) REVERT: C 380 PHE cc_start: 0.6676 (m-80) cc_final: 0.6415 (m-80) REVERT: C 432 GLN cc_start: 0.6170 (mt0) cc_final: 0.5943 (mp10) REVERT: C 947 SER cc_start: 0.8397 (m) cc_final: 0.8047 (p) outliers start: 44 outliers final: 26 residues processed: 312 average time/residue: 0.1759 time to fit residues: 86.4883 Evaluate side-chains 228 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 1038 HIS 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 210 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 42 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 228 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 chunk 140 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 257 optimal weight: 0.0170 chunk 279 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 205 GLN B 226 GLN B 949 ASN C 194 HIS C 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.176825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119056 restraints weight = 41954.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116353 restraints weight = 26809.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115968 restraints weight = 22596.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116613 restraints weight = 21931.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116568 restraints weight = 20403.523| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25921 Z= 0.159 Angle : 0.680 13.083 35338 Z= 0.355 Chirality : 0.048 0.301 4094 Planarity : 0.004 0.070 4535 Dihedral : 5.795 59.196 4202 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 1.51 % Allowed : 8.28 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 3147 helix: 1.65 (0.21), residues: 627 sheet: -0.07 (0.20), residues: 617 loop : -1.47 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 201 TYR 0.022 0.001 TYR B1047 PHE 0.029 0.002 PHE C 380 TRP 0.019 0.001 TRP C 416 HIS 0.006 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00353 (25883) covalent geometry : angle 0.65694 (35224) hydrogen bonds : bond 0.05016 ( 903) hydrogen bonds : angle 5.81709 ( 2553) link_NAG-ASN : bond 0.00588 ( 38) link_NAG-ASN : angle 3.15173 ( 114) *********************** 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 267 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6722 (tt) REVERT: A 113 VAL cc_start: 0.7162 (p) cc_final: 0.6823 (p) REVERT: A 164 MET cc_start: 0.5766 (tpt) cc_final: 0.5172 (mmm) REVERT: A 181 PHE cc_start: 0.6477 (t80) cc_final: 0.5851 (t80) REVERT: A 188 PHE cc_start: 0.6670 (m-80) cc_final: 0.6454 (m-80) REVERT: A 371 CYS cc_start: 0.8181 (m) cc_final: 0.7804 (m) REVERT: A 495 PHE cc_start: 0.5968 (m-80) cc_final: 0.5517 (m-10) REVERT: B 179 PHE cc_start: 0.7943 (m-80) cc_final: 0.7643 (m-80) REVERT: B 249 TYR cc_start: 0.7231 (m-80) cc_final: 0.6564 (m-80) REVERT: B 547 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.6970 (mmm-85) REVERT: B 836 ASN cc_start: 0.8116 (m110) cc_final: 0.7842 (m110) REVERT: B 929 GLN cc_start: 0.8380 (tp40) cc_final: 0.8112 (mm-40) REVERT: C 192 SER cc_start: 0.8402 (p) cc_final: 0.8051 (t) REVERT: C 269 VAL cc_start: 0.8712 (t) cc_final: 0.8477 (m) REVERT: C 293 TYR cc_start: 0.8109 (m-80) cc_final: 0.7905 (m-80) REVERT: C 296 SER cc_start: 0.8172 (t) cc_final: 0.7817 (m) REVERT: C 297 ASN cc_start: 0.8295 (m-40) cc_final: 0.7966 (m-40) REVERT: C 333 TRP cc_start: 0.5414 (p90) cc_final: 0.5094 (p90) REVERT: C 369 ASP cc_start: 0.7543 (m-30) cc_final: 0.7222 (m-30) REVERT: C 380 PHE cc_start: 0.6622 (m-80) cc_final: 0.6368 (m-10) REVERT: C 432 GLN cc_start: 0.6062 (mt0) cc_final: 0.5793 (mp10) REVERT: C 947 SER cc_start: 0.8314 (m) cc_final: 0.7991 (p) outliers start: 42 outliers final: 24 residues processed: 261 average time/residue: 0.1554 time to fit residues: 65.4155 Evaluate side-chains 226 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 279 THR 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 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 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 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 653 SER Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 956 VAL 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 196 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 145 optimal weight: 30.0000 chunk 180 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 881 GLN ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 894 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113893 restraints weight = 41664.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114622 restraints weight = 27227.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114383 restraints weight = 20207.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114593 restraints weight = 19023.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114744 restraints weight = 17685.548| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25921 Z= 0.162 Angle : 0.665 12.407 35338 Z= 0.345 Chirality : 0.048 0.315 4094 Planarity : 0.004 0.052 4535 Dihedral : 5.801 59.845 4202 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 1.80 % Allowed : 8.78 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.15), residues: 3147 helix: 1.63 (0.21), residues: 627 sheet: -0.21 (0.19), residues: 625 loop : -1.55 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 34 TYR 0.023 0.001 TYR B1047 PHE 0.028 0.002 PHE C 521 TRP 0.013 0.001 TRP C 416 HIS 0.005 0.001 HIS B1063 Details of bonding type rmsd covalent geometry : bond 0.00369 (25883) covalent geometry : angle 0.64387 (35224) hydrogen bonds : bond 0.04689 ( 903) hydrogen bonds : angle 5.66357 ( 2553) link_NAG-ASN : bond 0.00575 ( 38) link_NAG-ASN : angle 3.01011 ( 114) *********************** 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 275 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.868 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 56 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6681 (tp) REVERT: A 164 MET cc_start: 0.5655 (tpt) cc_final: 0.5114 (mmm) REVERT: A 178 GLU cc_start: 0.7830 (mp0) cc_final: 0.7608 (mp0) REVERT: A 181 PHE cc_start: 0.6411 (t80) cc_final: 0.5875 (t80) REVERT: A 337 ARG cc_start: 0.6739 (mmp-170) cc_final: 0.6478 (mmp-170) REVERT: A 371 CYS cc_start: 0.8074 (m) cc_final: 0.7873 (m) REVERT: A 495 PHE cc_start: 0.6037 (m-80) cc_final: 0.5466 (m-10) REVERT: A 682 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 249 TYR cc_start: 0.7187 (m-80) cc_final: 0.6554 (m-80) REVERT: B 547 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7046 (mmm-85) REVERT: B 836 ASN cc_start: 0.8125 (m110) cc_final: 0.7847 (m110) REVERT: B 929 GLN cc_start: 0.8408 (tp40) cc_final: 0.8145 (mm-40) REVERT: B 963 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7699 (ttm170) REVERT: C 192 SER cc_start: 0.8350 (p) cc_final: 0.8066 (t) REVERT: C 210 LEU cc_start: 0.7823 (mt) cc_final: 0.7515 (mm) REVERT: C 250 LEU cc_start: 0.7213 (mp) cc_final: 0.6868 (mp) REVERT: C 296 SER cc_start: 0.8163 (t) cc_final: 0.7836 (m) REVERT: C 297 ASN cc_start: 0.8214 (m-40) cc_final: 0.7894 (m-40) REVERT: C 333 TRP cc_start: 0.5338 (p90) cc_final: 0.5047 (p90) REVERT: C 369 ASP cc_start: 0.7514 (m-30) cc_final: 0.7187 (m-30) REVERT: C 432 GLN cc_start: 0.5945 (mt0) cc_final: 0.5708 (mp10) REVERT: C 947 SER cc_start: 0.8523 (m) cc_final: 0.8148 (p) outliers start: 50 outliers final: 32 residues processed: 264 average time/residue: 0.1549 time to fit residues: 66.4690 Evaluate side-chains 230 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 279 THR 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 298 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1052 GLU 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 552 THR Chi-restraints excluded: chain C residue 653 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 311 optimal weight: 0.2980 chunk 254 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116918 restraints weight = 41659.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112820 restraints weight = 28941.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113825 restraints weight = 22817.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114055 restraints weight = 22868.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114087 restraints weight = 20976.425| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25921 Z= 0.168 Angle : 0.663 12.473 35338 Z= 0.341 Chirality : 0.048 0.321 4094 Planarity : 0.004 0.049 4535 Dihedral : 5.800 59.922 4202 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 2.09 % Allowed : 9.28 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 3147 helix: 1.71 (0.21), residues: 626 sheet: -0.41 (0.20), residues: 629 loop : -1.60 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 201 TYR 0.023 0.001 TYR B1047 PHE 0.029 0.002 PHE C 521 TRP 0.026 0.002 TRP C 416 HIS 0.008 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00385 (25883) covalent geometry : angle 0.64124 (35224) hydrogen bonds : bond 0.04558 ( 903) hydrogen bonds : angle 5.59210 ( 2553) link_NAG-ASN : bond 0.00520 ( 38) link_NAG-ASN : angle 3.00463 ( 114) *********************** 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 271 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.973 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 56 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6566 (tp) REVERT: A 74 ASN cc_start: 0.4640 (OUTLIER) cc_final: 0.3568 (t0) REVERT: A 164 MET cc_start: 0.5749 (tpt) cc_final: 0.5132 (mmm) REVERT: A 178 GLU cc_start: 0.7811 (mp0) cc_final: 0.7571 (mp0) REVERT: A 371 CYS cc_start: 0.8085 (m) cc_final: 0.7787 (m) REVERT: A 380 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.4665 (m-80) REVERT: A 383 ARG cc_start: 0.3447 (ttt90) cc_final: 0.3194 (tpt-90) REVERT: B 249 TYR cc_start: 0.7116 (m-80) cc_final: 0.6527 (m-80) REVERT: B 547 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7213 (mmm-85) REVERT: B 836 ASN cc_start: 0.8144 (m110) cc_final: 0.7859 (m110) REVERT: B 963 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7808 (ttm170) REVERT: C 192 SER cc_start: 0.8352 (p) cc_final: 0.8117 (t) REVERT: C 210 LEU cc_start: 0.7827 (mt) cc_final: 0.7495 (mm) REVERT: C 293 TYR cc_start: 0.8247 (m-80) cc_final: 0.7771 (m-80) REVERT: C 296 SER cc_start: 0.8209 (t) cc_final: 0.7886 (m) REVERT: C 297 ASN cc_start: 0.8117 (m-40) cc_final: 0.7760 (m110) REVERT: C 369 ASP cc_start: 0.7511 (m-30) cc_final: 0.7191 (m-30) REVERT: C 970 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7820 (tt0) outliers start: 58 outliers final: 39 residues processed: 256 average time/residue: 0.1641 time to fit residues: 69.2175 Evaluate side-chains 235 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 74 ASN 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 279 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 526 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 740 CYS 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 298 PHE Chi-restraints excluded: chain B residue 834 LYS 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 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 542 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 800 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 HIS ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115997 restraints weight = 41703.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115154 restraints weight = 25668.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114491 restraints weight = 19397.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115224 restraints weight = 22067.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115207 restraints weight = 18285.166| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3750 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= 0.139 Angle : 0.642 12.511 35338 Z= 0.331 Chirality : 0.047 0.322 4094 Planarity : 0.004 0.046 4535 Dihedral : 5.692 58.811 4202 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.51 % Favored : 93.39 % Rotamer: Outliers : 1.91 % Allowed : 9.90 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3147 helix: 1.79 (0.21), residues: 626 sheet: -0.44 (0.20), residues: 622 loop : -1.58 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.021 0.001 TYR C 403 PHE 0.026 0.001 PHE B 225 TRP 0.017 0.001 TRP C 416 HIS 0.007 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00309 (25883) covalent geometry : angle 0.62199 (35224) hydrogen bonds : bond 0.04343 ( 903) hydrogen bonds : angle 5.48815 ( 2553) link_NAG-ASN : bond 0.00491 ( 38) link_NAG-ASN : angle 2.89570 ( 114) *********************** 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 260 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6416 (tp) REVERT: A 78 TYR cc_start: 0.5251 (t80) cc_final: 0.4906 (t80) REVERT: A 164 MET cc_start: 0.5750 (tpt) cc_final: 0.5102 (mmm) REVERT: A 178 GLU cc_start: 0.7831 (mp0) cc_final: 0.7590 (mp0) REVERT: A 371 CYS cc_start: 0.8106 (m) cc_final: 0.7843 (m) REVERT: A 380 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4700 (m-80) REVERT: A 383 ARG cc_start: 0.3632 (ttt90) cc_final: 0.3350 (tpt-90) REVERT: A 567 ILE cc_start: 0.8022 (mt) cc_final: 0.7797 (mt) REVERT: B 249 TYR cc_start: 0.7193 (m-80) cc_final: 0.6622 (m-80) REVERT: B 547 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: B 836 ASN cc_start: 0.8145 (m110) cc_final: 0.7861 (m110) REVERT: B 963 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7835 (ttm170) REVERT: C 210 LEU cc_start: 0.7795 (mt) cc_final: 0.7577 (mm) REVERT: C 293 TYR cc_start: 0.8254 (m-80) cc_final: 0.7808 (m-80) REVERT: C 296 SER cc_start: 0.8196 (t) cc_final: 0.7851 (m) REVERT: C 297 ASN cc_start: 0.8140 (m-40) cc_final: 0.7762 (m110) REVERT: C 369 ASP cc_start: 0.7466 (m-30) cc_final: 0.7162 (m-30) REVERT: C 473 GLN cc_start: 0.6648 (mm-40) cc_final: 0.5826 (mt0) REVERT: C 882 MET cc_start: 0.8613 (tpt) cc_final: 0.8311 (mmm) outliers start: 53 outliers final: 40 residues processed: 246 average time/residue: 0.1591 time to fit residues: 64.3417 Evaluate side-chains 238 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 176 LEU 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 296 SER Chi-restraints excluded: chain A residue 380 PHE 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 B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 LEU 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 834 LYS 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 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 218 ILE 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 495 PHE Chi-restraints excluded: chain C residue 552 THR 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 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1085 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 99 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 241 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 293 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** C 183 ASN ** 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 = 0.4265 r_free = 0.4265 target = 0.176020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116127 restraints weight = 41542.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116010 restraints weight = 25926.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115477 restraints weight = 19222.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115844 restraints weight = 19957.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115959 restraints weight = 17972.656| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25921 Z= 0.130 Angle : 0.627 12.574 35338 Z= 0.322 Chirality : 0.046 0.321 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.605 58.446 4202 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.20 % Allowed : 9.97 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3147 helix: 1.85 (0.21), residues: 627 sheet: -0.49 (0.20), residues: 591 loop : -1.58 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.020 0.001 TYR C 403 PHE 0.035 0.001 PHE C 521 TRP 0.030 0.001 TRP C 416 HIS 0.003 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00287 (25883) covalent geometry : angle 0.60723 (35224) hydrogen bonds : bond 0.04164 ( 903) hydrogen bonds : angle 5.39342 ( 2553) link_NAG-ASN : bond 0.00486 ( 38) link_NAG-ASN : angle 2.80852 ( 114) *********************** 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 268 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.761 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 56 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6303 (tp) REVERT: A 78 TYR cc_start: 0.5091 (t80) cc_final: 0.4787 (t80) REVERT: A 164 MET cc_start: 0.5801 (tpt) cc_final: 0.5096 (mmm) REVERT: A 178 GLU cc_start: 0.7824 (mp0) cc_final: 0.7566 (mp0) REVERT: A 371 CYS cc_start: 0.8111 (m) cc_final: 0.7810 (m) REVERT: A 380 PHE cc_start: 0.5141 (OUTLIER) cc_final: 0.4756 (m-80) REVERT: A 383 ARG cc_start: 0.3699 (ttt90) cc_final: 0.3424 (tpt-90) REVERT: A 567 ILE cc_start: 0.8043 (mt) cc_final: 0.7832 (mt) REVERT: B 249 TYR cc_start: 0.7153 (m-80) cc_final: 0.6617 (m-80) REVERT: B 547 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7251 (mmm-85) REVERT: B 836 ASN cc_start: 0.8125 (m110) cc_final: 0.7828 (m110) REVERT: B 963 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7779 (ttm170) REVERT: C 293 TYR cc_start: 0.8233 (m-80) cc_final: 0.7824 (m-80) REVERT: C 296 SER cc_start: 0.8130 (t) cc_final: 0.7833 (m) REVERT: C 297 ASN cc_start: 0.8043 (m-40) cc_final: 0.7652 (m110) REVERT: C 369 ASP cc_start: 0.7413 (m-30) cc_final: 0.7119 (m-30) REVERT: C 473 GLN cc_start: 0.6660 (mm-40) cc_final: 0.5806 (mt0) REVERT: C 970 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7745 (tt0) outliers start: 61 outliers final: 41 residues processed: 252 average time/residue: 0.1373 time to fit residues: 57.1053 Evaluate side-chains 238 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 176 LEU 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 450 THR 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 918 LEU 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 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1052 GLU 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 381 VAL 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 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 1084 VAL Chi-restraints excluded: chain C residue 1085 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 251 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS A1038 HIS B 49 HIS ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 635 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.172764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114486 restraints weight = 41763.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111477 restraints weight = 27531.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111273 restraints weight = 23244.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111522 restraints weight = 22423.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111599 restraints weight = 20547.037| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 25921 Z= 0.240 Angle : 0.695 12.479 35338 Z= 0.356 Chirality : 0.049 0.324 4094 Planarity : 0.004 0.043 4535 Dihedral : 5.935 58.527 4202 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 2.34 % Allowed : 10.47 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.15), residues: 3147 helix: 1.59 (0.21), residues: 627 sheet: -0.69 (0.20), residues: 603 loop : -1.76 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 253 TYR 0.029 0.002 TYR C 376 PHE 0.034 0.002 PHE C 521 TRP 0.031 0.002 TRP C 416 HIS 0.005 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00570 (25883) covalent geometry : angle 0.67403 (35224) hydrogen bonds : bond 0.04684 ( 903) hydrogen bonds : angle 5.58085 ( 2553) link_NAG-ASN : bond 0.00435 ( 38) link_NAG-ASN : angle 3.04258 ( 114) *********************** 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 261 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6504 (tp) REVERT: A 164 MET cc_start: 0.5463 (tpt) cc_final: 0.4821 (mmm) REVERT: A 178 GLU cc_start: 0.7834 (mp0) cc_final: 0.7565 (mp0) REVERT: A 371 CYS cc_start: 0.8119 (m) cc_final: 0.7883 (m) REVERT: A 380 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4771 (m-80) REVERT: A 490 VAL cc_start: 0.6700 (OUTLIER) cc_final: 0.6206 (m) REVERT: A 544 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6082 (pt0) REVERT: A 567 ILE cc_start: 0.8111 (mt) cc_final: 0.7903 (mt) REVERT: A 1038 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.8106 (m-70) REVERT: B 249 TYR cc_start: 0.7173 (m-80) cc_final: 0.6653 (m-80) REVERT: B 547 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7158 (mmm-85) REVERT: B 836 ASN cc_start: 0.8190 (m110) cc_final: 0.7916 (m110) REVERT: B 963 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7816 (ttm170) REVERT: C 296 SER cc_start: 0.8204 (t) cc_final: 0.7931 (t) REVERT: C 297 ASN cc_start: 0.8104 (m-40) cc_final: 0.7811 (m110) REVERT: C 369 ASP cc_start: 0.7559 (m-30) cc_final: 0.7256 (m-30) REVERT: C 473 GLN cc_start: 0.6386 (mm-40) cc_final: 0.5715 (mt0) outliers start: 65 outliers final: 43 residues processed: 243 average time/residue: 0.1404 time to fit residues: 56.7664 Evaluate side-chains 236 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 187 TYR 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 740 CYS 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 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE 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 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 485 TYR Chi-restraints excluded: chain C residue 552 THR 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 1021 ASP 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 207 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 264 optimal weight: 0.0040 chunk 266 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN C 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121189 restraints weight = 41771.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120391 restraints weight = 36886.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120698 restraints weight = 24609.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119298 restraints weight = 18989.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119527 restraints weight = 21207.022| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4122 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= 0.139 Angle : 0.646 12.374 35338 Z= 0.331 Chirality : 0.047 0.320 4094 Planarity : 0.004 0.048 4535 Dihedral : 5.761 58.987 4202 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.64 % Favored : 93.26 % Rotamer: Outliers : 1.84 % Allowed : 11.23 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 3147 helix: 1.77 (0.21), residues: 625 sheet: -0.60 (0.20), residues: 597 loop : -1.75 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.020 0.001 TYR B1047 PHE 0.032 0.002 PHE C 521 TRP 0.027 0.002 TRP C 416 HIS 0.024 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00313 (25883) covalent geometry : angle 0.62607 (35224) hydrogen bonds : bond 0.04286 ( 903) hydrogen bonds : angle 5.43945 ( 2553) link_NAG-ASN : bond 0.00465 ( 38) link_NAG-ASN : angle 2.89655 ( 114) *********************** 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 246 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6415 (tp) REVERT: A 78 TYR cc_start: 0.5116 (t80) cc_final: 0.4880 (t80) REVERT: A 164 MET cc_start: 0.5567 (tpt) cc_final: 0.4971 (mmm) REVERT: A 371 CYS cc_start: 0.8088 (m) cc_final: 0.7794 (m) REVERT: A 490 VAL cc_start: 0.6780 (OUTLIER) cc_final: 0.6484 (m) REVERT: B 547 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7378 (mmm-85) REVERT: B 836 ASN cc_start: 0.8059 (m110) cc_final: 0.7813 (m110) REVERT: C 187 TYR cc_start: 0.6183 (t80) cc_final: 0.5895 (t80) REVERT: C 296 SER cc_start: 0.8144 (t) cc_final: 0.7892 (t) REVERT: C 297 ASN cc_start: 0.8076 (m-40) cc_final: 0.7779 (m110) REVERT: C 369 ASP cc_start: 0.7283 (m-30) cc_final: 0.7004 (m-30) REVERT: C 970 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7647 (tt0) outliers start: 51 outliers final: 44 residues processed: 230 average time/residue: 0.1365 time to fit residues: 52.3722 Evaluate side-chains 233 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 187 TYR 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 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 918 LEU 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 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU 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 485 TYR Chi-restraints excluded: chain C residue 495 PHE 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 800 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 91 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 164 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122575 restraints weight = 41763.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122068 restraints weight = 44201.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119059 restraints weight = 29112.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117498 restraints weight = 25138.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118153 restraints weight = 26126.215| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 25921 Z= 0.188 Angle : 0.674 12.120 35338 Z= 0.345 Chirality : 0.048 0.324 4094 Planarity : 0.004 0.043 4535 Dihedral : 5.920 59.969 4202 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 1.73 % Allowed : 11.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3147 helix: 1.68 (0.21), residues: 625 sheet: -0.72 (0.20), residues: 589 loop : -1.83 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 383 TYR 0.025 0.002 TYR B1047 PHE 0.031 0.002 PHE C 521 TRP 0.027 0.002 TRP C 416 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00443 (25883) covalent geometry : angle 0.65281 (35224) hydrogen bonds : bond 0.04486 ( 903) hydrogen bonds : angle 5.49962 ( 2553) link_NAG-ASN : bond 0.00440 ( 38) link_NAG-ASN : angle 2.98992 ( 114) ********************** 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 238 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6621 (tp) REVERT: A 78 TYR cc_start: 0.5168 (t80) cc_final: 0.4910 (t80) REVERT: A 164 MET cc_start: 0.5388 (tpt) cc_final: 0.4890 (mmm) REVERT: A 371 CYS cc_start: 0.7969 (m) cc_final: 0.7688 (m) REVERT: B 547 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: B 836 ASN cc_start: 0.8115 (m110) cc_final: 0.7856 (m110) REVERT: C 296 SER cc_start: 0.8163 (t) cc_final: 0.7904 (t) REVERT: C 297 ASN cc_start: 0.8076 (m-40) cc_final: 0.7772 (m110) REVERT: C 369 ASP cc_start: 0.7316 (m-30) cc_final: 0.7044 (m-30) REVERT: C 473 GLN cc_start: 0.4578 (mt0) cc_final: 0.3728 (tm-30) outliers start: 48 outliers final: 45 residues processed: 223 average time/residue: 0.1553 time to fit residues: 58.1254 Evaluate side-chains 228 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 187 TYR 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 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 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 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU 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 485 TYR Chi-restraints excluded: chain C residue 495 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 237 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 197 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 238 optimal weight: 0.1980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.174118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121652 restraints weight = 41660.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119414 restraints weight = 40747.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120489 restraints weight = 29983.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119067 restraints weight = 24184.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119382 restraints weight = 21504.274| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 25921 Z= 0.160 Angle : 0.655 12.261 35338 Z= 0.335 Chirality : 0.047 0.322 4094 Planarity : 0.004 0.043 4535 Dihedral : 5.849 59.274 4202 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 1.87 % Allowed : 11.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.15), residues: 3147 helix: 1.72 (0.21), residues: 625 sheet: -0.70 (0.20), residues: 592 loop : -1.84 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 383 TYR 0.023 0.001 TYR B1047 PHE 0.031 0.002 PHE C 521 TRP 0.026 0.002 TRP C 416 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00371 (25883) covalent geometry : angle 0.63486 (35224) hydrogen bonds : bond 0.04322 ( 903) hydrogen bonds : angle 5.42304 ( 2553) link_NAG-ASN : bond 0.00449 ( 38) link_NAG-ASN : angle 2.93341 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.42 seconds wall clock time: 85 minutes 51.66 seconds (5151.66 seconds total)