Starting phenix.real_space_refine on Sun Jun 22 03:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu9_29456/06_2025/8fu9_29456_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16091 2.51 5 N 4185 2.21 5 O 4923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25313 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8265 Classifications: {'peptide': 1058} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "B" Number of atoms: 8262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'CIS': 5, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "C" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8254 Classifications: {'peptide': 1056} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 995} Chain breaks: 3 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.39, per 1000 atoms: 0.61 Number of scatterers: 25313 At special positions: 0 Unit cell: (143.971, 179.755, 160.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4923 8.00 N 4185 7.00 C 16091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 109 " " NAG A1202 " - " ASN A 262 " " NAG A1203 " - " ASN A 689 " " NAG A1204 " - " ASN A 697 " " NAG A1205 " - " ASN A 781 " " NAG A1206 " - " ASN A1054 " " NAG A1207 " - " ASN A1078 " " NAG A1208 " - " ASN A1114 " " NAG A1209 " - " ASN A 637 " " NAG A1210 " - " ASN A 583 " " NAG A1211 " - " ASN A 61 " " NAG A1212 " - " ASN A 596 " " NAG A1213 " - " ASN A 311 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 262 " " NAG B1203 " - " ASN B 596 " " NAG B1204 " - " ASN B 689 " " NAG B1205 " - " ASN B1054 " " NAG B1206 " - " ASN B 697 " " NAG B1207 " - " ASN B1078 " " NAG B1208 " - " ASN B1114 " " NAG B1209 " - " ASN B 637 " " NAG B1210 " - " ASN B 781 " " NAG B1211 " - " ASN B 583 " " NAG B1212 " - " ASN B 311 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 262 " " NAG C1203 " - " ASN C 596 " " NAG C1204 " - " ASN C 689 " " NAG C1205 " - " ASN C 697 " " NAG C1206 " - " ASN C 781 " " NAG C1207 " - " ASN C1054 " " NAG C1208 " - " ASN C1114 " " NAG C1209 " - " ASN C 323 " " NAG C1210 " - " ASN C 637 " " NAG C1211 " - " ASN C1078 " " NAG C1212 " - " ASN C 583 " " NAG C1213 " - " ASN C 311 " Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 3.1 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 23.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 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: 11.75 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4526 1.32 - 1.44: 6776 1.44 - 1.57: 14400 1.57 - 1.70: 36 1.70 - 1.82: 145 Bond restraints: 25883 Sorted by residual: bond pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " ideal model delta sigma weight residual 1.516 1.726 -0.210 2.50e-02 1.60e+03 7.06e+01 bond pdb=" N PRO C 487 " pdb=" CA PRO C 487 " ideal model delta sigma weight residual 1.473 1.442 0.031 8.50e-03 1.38e+04 1.33e+01 bond pdb=" CB ASN C 894 " pdb=" CG ASN C 894 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.27e+01 bond pdb=" CB LEU B 808 " pdb=" CG LEU B 808 " ideal model delta sigma weight residual 1.530 1.598 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB LEU B1125 " pdb=" CG LEU B1125 " ideal model delta sigma weight residual 1.530 1.596 -0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 25878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.21: 35216 9.21 - 18.42: 6 18.42 - 27.64: 0 27.64 - 36.85: 1 36.85 - 46.06: 1 Bond angle restraints: 35224 Sorted by residual: angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" OD1 ASN A 689 " ideal model delta sigma weight residual 120.80 74.74 46.06 2.00e+00 2.50e-01 5.30e+02 angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 116.40 85.25 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" OD1 ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 122.60 131.81 -9.21 1.00e+00 1.00e+00 8.48e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.23 -6.57 7.20e-01 1.93e+00 8.34e+01 angle pdb=" C GLU A 211 " pdb=" N PRO A 212 " pdb=" CA PRO A 212 " ideal model delta sigma weight residual 119.85 128.39 -8.54 1.01e+00 9.80e-01 7.15e+01 ... (remaining 35219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15229 17.71 - 35.42: 434 35.42 - 53.13: 98 53.13 - 70.85: 61 70.85 - 88.56: 28 Dihedral angle restraints: 15850 sinusoidal: 6615 harmonic: 9235 Sorted by residual: dihedral pdb=" CA THR B 921 " pdb=" C THR B 921 " pdb=" N PRO B 922 " pdb=" CA PRO B 922 " ideal model delta harmonic sigma weight residual -180.00 -143.46 -36.54 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ASP B1119 " pdb=" C ASP B1119 " pdb=" N PRO B1120 " pdb=" CA PRO B1120 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N ILE A 106 " pdb=" CA ILE A 106 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 15847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3122 0.079 - 0.157: 766 0.157 - 0.236: 146 0.236 - 0.314: 39 0.314 - 0.393: 21 Chirality restraints: 4094 Sorted by residual: chirality pdb=" C2 NAG B1201 " pdb=" C1 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" N2 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2 NAG B1203 " pdb=" C1 NAG B1203 " pdb=" C3 NAG B1203 " pdb=" N2 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1 NAG A1213 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG A1213 " pdb=" O5 NAG A1213 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4091 not shown) Planarity restraints: 4573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 pdb=" C1 NAG A1203 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 2.06e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 596 " 0.048 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" CG ASN B 596 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 596 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 596 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1203 " 0.058 2.00e-02 2.50e+03 ... (remaining 4570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5455 2.77 - 3.30: 23088 3.30 - 3.84: 40859 3.84 - 4.37: 48951 4.37 - 4.90: 81155 Nonbonded interactions: 199508 Sorted by model distance: nonbonded pdb=" OG1 THR C 33 " pdb=" O PRO C 204 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.280 3.040 nonbonded pdb=" N ASN A 689 " pdb=" OD1 ASN A 689 " model vdw 2.333 3.120 nonbonded pdb=" OG SER C 864 " pdb=" OG1 THR C 867 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A1103 " pdb=" N GLY A1104 " model vdw 2.353 3.120 ... (remaining 199503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) selection = (chain 'B' and (resid 14 through 807 or resid 834 through 1125 or resid 1201 thr \ ough 1212)) selection = (chain 'C' and (resid 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.870 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: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 58.940 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.210 25921 Z= 0.655 Angle : 1.353 46.062 35338 Z= 0.896 Chirality : 0.077 0.393 4094 Planarity : 0.006 0.206 4535 Dihedral : 10.901 88.557 9912 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.45 % Favored : 93.07 % Rotamer: Outliers : 0.14 % Allowed : 0.65 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3147 helix: 0.52 (0.19), residues: 624 sheet: 0.64 (0.21), residues: 560 loop : -1.26 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP A 866 HIS 0.005 0.001 HIS C 499 PHE 0.025 0.003 PHE B 122 TYR 0.035 0.004 TYR C 187 ARG 0.003 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.06241 ( 38) link_NAG-ASN : angle 2.47117 ( 114) hydrogen bonds : bond 0.17575 ( 903) hydrogen bonds : angle 7.96280 ( 2553) covalent geometry : bond 0.01185 (25883) covalent geometry : angle 1.34818 (35224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.4536 (m-80) cc_final: 0.2844 (m-80) REVERT: A 164 MET cc_start: 0.5980 (tpt) cc_final: 0.4901 (mmm) REVERT: A 176 LEU cc_start: 0.7641 (pp) cc_final: 0.7426 (pp) REVERT: A 544 GLN cc_start: 0.6350 (mm-40) cc_final: 0.5957 (mm110) REVERT: A 572 PHE cc_start: 0.7997 (p90) cc_final: 0.7759 (p90) REVERT: A 634 GLU cc_start: 0.8209 (tt0) cc_final: 0.7983 (tt0) REVERT: A 717 ASP cc_start: 0.7926 (t0) cc_final: 0.7720 (t0) REVERT: A 848 GLU cc_start: 0.8186 (mp0) cc_final: 0.7923 (mm-30) REVERT: B 79 PHE cc_start: 0.4919 (m-80) cc_final: 0.4374 (m-80) REVERT: B 179 PHE cc_start: 0.8205 (m-80) cc_final: 0.7952 (m-10) REVERT: B 187 TYR cc_start: 0.7370 (m-80) cc_final: 0.7068 (m-80) REVERT: B 249 TYR cc_start: 0.7436 (m-80) cc_final: 0.6971 (m-80) REVERT: B 517 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7061 (tptt) REVERT: B 552 THR cc_start: 0.7674 (p) cc_final: 0.7236 (m) REVERT: B 1116 THR cc_start: 0.8589 (m) cc_final: 0.8383 (p) REVERT: B 1118 TYR cc_start: 0.7152 (m-80) cc_final: 0.6838 (m-80) REVERT: C 193 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7782 (mmmt) REVERT: C 288 VAL cc_start: 0.8697 (t) cc_final: 0.8280 (t) REVERT: C 293 TYR cc_start: 0.8660 (m-80) cc_final: 0.8063 (m-80) REVERT: C 296 SER cc_start: 0.8309 (t) cc_final: 0.7754 (m) REVERT: C 297 ASN cc_start: 0.8550 (m-40) cc_final: 0.8109 (m-40) REVERT: C 333 TRP cc_start: 0.6253 (p90) cc_final: 0.5763 (p90) REVERT: C 369 ASP cc_start: 0.7792 (m-30) cc_final: 0.7451 (m-30) REVERT: C 432 GLN cc_start: 0.5805 (mt0) cc_final: 0.5401 (mp10) REVERT: C 754 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8612 (mp10) REVERT: C 836 ASN cc_start: 0.6947 (m-40) cc_final: 0.6690 (m110) REVERT: C 947 SER cc_start: 0.8700 (m) cc_final: 0.8475 (p) REVERT: C 985 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8291 (tp40) outliers start: 4 outliers final: 2 residues processed: 541 average time/residue: 0.3952 time to fit residues: 327.5020 Evaluate side-chains 256 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain C residue 1054 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.1980 chunk 183 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 HIS A 935 ASN A 990 GLN A1038 HIS B 670 GLN B 836 ASN B 937 GLN C 205 GLN C 594 ASN C 990 GLN C1081 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118781 restraints weight = 41089.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120327 restraints weight = 24634.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121820 restraints weight = 17839.157| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25921 Z= 0.155 Angle : 0.734 13.437 35338 Z= 0.386 Chirality : 0.049 0.285 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.924 58.865 4204 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 5.97 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3147 helix: 1.64 (0.21), residues: 624 sheet: 0.20 (0.20), residues: 637 loop : -1.42 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 866 HIS 0.012 0.001 HIS B 49 PHE 0.032 0.002 PHE C 380 TYR 0.022 0.002 TYR B1047 ARG 0.006 0.000 ARG A 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 38) link_NAG-ASN : angle 3.33246 ( 114) hydrogen bonds : bond 0.05368 ( 903) hydrogen bonds : angle 6.16223 ( 2553) covalent geometry : bond 0.00331 (25883) covalent geometry : angle 0.71034 (35224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.7225 (p) cc_final: 0.6918 (p) REVERT: A 164 MET cc_start: 0.5730 (tpt) cc_final: 0.5407 (mmm) REVERT: A 176 LEU cc_start: 0.7445 (pp) cc_final: 0.6937 (pp) REVERT: A 178 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6690 (mp0) REVERT: A 181 PHE cc_start: 0.6482 (t80) cc_final: 0.5967 (t80) REVERT: A 371 CYS cc_start: 0.8121 (m) cc_final: 0.7835 (m) REVERT: B 179 PHE cc_start: 0.7981 (m-80) cc_final: 0.7599 (m-80) REVERT: B 249 TYR cc_start: 0.7259 (m-80) cc_final: 0.6617 (m-80) REVERT: B 547 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6893 (mmm-85) REVERT: B 836 ASN cc_start: 0.8134 (m110) cc_final: 0.7847 (m110) REVERT: B 849 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7234 (mtm) REVERT: C 269 VAL cc_start: 0.8757 (t) cc_final: 0.8510 (m) REVERT: C 296 SER cc_start: 0.8206 (t) cc_final: 0.7824 (m) REVERT: C 297 ASN cc_start: 0.8264 (m-40) cc_final: 0.8028 (m-40) REVERT: C 333 TRP cc_start: 0.5589 (p90) cc_final: 0.5079 (p90) REVERT: C 369 ASP cc_start: 0.7509 (m-30) cc_final: 0.7167 (m-30) REVERT: C 380 PHE cc_start: 0.6605 (m-80) cc_final: 0.6310 (m-80) REVERT: C 432 GLN cc_start: 0.6024 (mt0) cc_final: 0.5776 (mp10) REVERT: C 947 SER cc_start: 0.8396 (m) cc_final: 0.8042 (p) outliers start: 43 outliers final: 24 residues processed: 323 average time/residue: 0.3843 time to fit residues: 195.1692 Evaluate side-chains 236 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 232 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 935 ASN ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.176629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117789 restraints weight = 41499.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115903 restraints weight = 27013.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115411 restraints weight = 25100.547| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25921 Z= 0.174 Angle : 0.684 12.977 35338 Z= 0.357 Chirality : 0.048 0.310 4094 Planarity : 0.004 0.066 4535 Dihedral : 5.801 59.930 4202 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 1.58 % Allowed : 8.38 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3147 helix: 1.66 (0.21), residues: 627 sheet: -0.08 (0.20), residues: 624 loop : -1.46 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 416 HIS 0.005 0.001 HIS B 49 PHE 0.029 0.002 PHE C 380 TYR 0.024 0.002 TYR B1047 ARG 0.017 0.001 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 38) link_NAG-ASN : angle 3.16346 ( 114) hydrogen bonds : bond 0.04986 ( 903) hydrogen bonds : angle 5.80004 ( 2553) covalent geometry : bond 0.00386 (25883) covalent geometry : angle 0.66065 (35224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 2.529 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 113 VAL cc_start: 0.7218 (p) cc_final: 0.6865 (p) REVERT: A 164 MET cc_start: 0.5818 (tpt) cc_final: 0.5171 (mmm) REVERT: A 176 LEU cc_start: 0.7258 (pp) cc_final: 0.6661 (pp) REVERT: A 178 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6650 (mp0) REVERT: A 181 PHE cc_start: 0.6622 (t80) cc_final: 0.6120 (t80) REVERT: A 371 CYS cc_start: 0.8043 (m) cc_final: 0.7755 (m) REVERT: A 376 TYR cc_start: 0.5627 (m-80) cc_final: 0.5356 (m-80) REVERT: A 495 PHE cc_start: 0.5961 (m-80) cc_final: 0.5509 (m-10) REVERT: A 544 GLN cc_start: 0.6374 (mm-40) cc_final: 0.5974 (pt0) REVERT: A 682 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 179 PHE cc_start: 0.7936 (m-80) cc_final: 0.7628 (m-80) REVERT: B 193 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7339 (ttmm) REVERT: B 249 TYR cc_start: 0.7270 (m-80) cc_final: 0.6552 (m-80) REVERT: B 547 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.6914 (mmm-85) REVERT: B 836 ASN cc_start: 0.8164 (m110) cc_final: 0.7897 (m110) REVERT: B 929 GLN cc_start: 0.8414 (tp40) cc_final: 0.8149 (mm-40) REVERT: C 250 LEU cc_start: 0.7391 (mp) cc_final: 0.7086 (mp) REVERT: C 269 VAL cc_start: 0.8707 (t) cc_final: 0.8489 (m) REVERT: C 296 SER cc_start: 0.8183 (t) cc_final: 0.7831 (m) REVERT: C 297 ASN cc_start: 0.8313 (m-40) cc_final: 0.7991 (m-40) REVERT: C 369 ASP cc_start: 0.7531 (m-30) cc_final: 0.7197 (m-30) REVERT: C 432 GLN cc_start: 0.5949 (mt0) cc_final: 0.5670 (mp10) REVERT: C 947 SER cc_start: 0.8343 (m) cc_final: 0.7999 (p) outliers start: 44 outliers final: 26 residues processed: 277 average time/residue: 0.3384 time to fit residues: 151.6331 Evaluate side-chains 230 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 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 715 SER Chi-restraints excluded: chain B residue 838 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 311 optimal weight: 0.8980 chunk 313 optimal weight: 0.0020 chunk 21 optimal weight: 10.0000 chunk 230 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 A 935 ASN B 881 GLN ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 194 HIS C 635 HIS C 894 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.174831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117494 restraints weight = 41942.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114111 restraints weight = 27893.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113869 restraints weight = 22403.362| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25921 Z= 0.182 Angle : 0.680 12.391 35338 Z= 0.352 Chirality : 0.048 0.316 4094 Planarity : 0.004 0.061 4535 Dihedral : 5.881 59.710 4202 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 1.87 % Allowed : 9.10 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3147 helix: 1.60 (0.21), residues: 628 sheet: -0.19 (0.20), residues: 608 loop : -1.61 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 416 HIS 0.006 0.001 HIS A 232 PHE 0.029 0.002 PHE C 521 TYR 0.024 0.002 TYR B1047 ARG 0.007 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 38) link_NAG-ASN : angle 3.05072 ( 114) hydrogen bonds : bond 0.04747 ( 903) hydrogen bonds : angle 5.71581 ( 2553) covalent geometry : bond 0.00415 (25883) covalent geometry : angle 0.65875 (35224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.4439 (OUTLIER) cc_final: 0.3272 (t0) REVERT: A 164 MET cc_start: 0.5773 (tpt) cc_final: 0.5207 (mmm) REVERT: A 176 LEU cc_start: 0.7367 (pp) cc_final: 0.7024 (pp) REVERT: A 178 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6497 (mp0) REVERT: A 371 CYS cc_start: 0.8134 (m) cc_final: 0.7814 (m) REVERT: A 495 PHE cc_start: 0.6186 (m-80) cc_final: 0.5681 (m-10) REVERT: B 193 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7307 (ttmm) REVERT: B 249 TYR cc_start: 0.7190 (m-80) cc_final: 0.6583 (m-80) REVERT: B 547 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7143 (mmm-85) REVERT: B 836 ASN cc_start: 0.8145 (m110) cc_final: 0.7886 (m110) REVERT: B 929 GLN cc_start: 0.8425 (tp40) cc_final: 0.8144 (mm-40) REVERT: B 963 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7760 (ttm170) REVERT: C 192 SER cc_start: 0.8366 (p) cc_final: 0.8063 (t) REVERT: C 210 LEU cc_start: 0.7819 (mt) cc_final: 0.7500 (mm) REVERT: C 269 VAL cc_start: 0.8749 (t) cc_final: 0.8547 (m) REVERT: C 293 TYR cc_start: 0.8232 (m-80) cc_final: 0.7837 (m-80) REVERT: C 296 SER cc_start: 0.8152 (t) cc_final: 0.7862 (m) REVERT: C 297 ASN cc_start: 0.8205 (m-40) cc_final: 0.7873 (m110) REVERT: C 333 TRP cc_start: 0.5702 (p90) cc_final: 0.5241 (p90) REVERT: C 369 ASP cc_start: 0.7525 (m-30) cc_final: 0.7201 (m-30) REVERT: C 380 PHE cc_start: 0.6638 (m-80) cc_final: 0.6337 (m-80) REVERT: C 915 GLN cc_start: 0.8141 (pm20) cc_final: 0.7916 (pm20) REVERT: C 947 SER cc_start: 0.8475 (m) cc_final: 0.8104 (p) outliers start: 52 outliers final: 37 residues processed: 262 average time/residue: 0.3452 time to fit residues: 146.6896 Evaluate side-chains 231 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 ASN 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 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 759 GLN 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 105 LEU 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 920 SER Chi-restraints excluded: chain C residue 953 ILE Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 162 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 200 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 HIS ** 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 = 0.4265 r_free = 0.4265 target = 0.176048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117813 restraints weight = 41858.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115414 restraints weight = 26949.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115323 restraints weight = 20886.831| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25921 Z= 0.133 Angle : 0.636 13.193 35338 Z= 0.328 Chirality : 0.047 0.320 4094 Planarity : 0.004 0.056 4535 Dihedral : 5.681 58.600 4202 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.64 % Favored : 93.26 % Rotamer: Outliers : 1.91 % Allowed : 9.64 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3147 helix: 1.83 (0.21), residues: 626 sheet: -0.39 (0.19), residues: 629 loop : -1.57 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 416 HIS 0.007 0.001 HIS A 232 PHE 0.023 0.001 PHE C 521 TYR 0.020 0.001 TYR C 403 ARG 0.008 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 38) link_NAG-ASN : angle 2.91444 ( 114) hydrogen bonds : bond 0.04362 ( 903) hydrogen bonds : angle 5.52872 ( 2553) covalent geometry : bond 0.00286 (25883) covalent geometry : angle 0.61506 (35224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5800 (tpt) cc_final: 0.5204 (mmm) REVERT: A 178 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6528 (mp0) REVERT: A 371 CYS cc_start: 0.8141 (m) cc_final: 0.7859 (m) REVERT: A 380 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4613 (m-80) REVERT: A 495 PHE cc_start: 0.6046 (m-80) cc_final: 0.5536 (m-10) REVERT: B 193 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7303 (ttmm) REVERT: B 249 TYR cc_start: 0.7150 (m-80) cc_final: 0.6609 (m-80) REVERT: B 547 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7103 (mmm-85) REVERT: B 836 ASN cc_start: 0.8187 (m110) cc_final: 0.7904 (m110) REVERT: B 963 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7623 (ttm170) REVERT: C 192 SER cc_start: 0.8378 (p) cc_final: 0.8097 (t) REVERT: C 210 LEU cc_start: 0.7783 (mt) cc_final: 0.7514 (mm) REVERT: C 293 TYR cc_start: 0.8206 (m-80) cc_final: 0.7876 (m-80) REVERT: C 296 SER cc_start: 0.8163 (t) cc_final: 0.7855 (m) REVERT: C 297 ASN cc_start: 0.8137 (m-40) cc_final: 0.7777 (m110) REVERT: C 333 TRP cc_start: 0.5520 (p90) cc_final: 0.5159 (p90) REVERT: C 369 ASP cc_start: 0.7475 (m-30) cc_final: 0.7158 (m-30) outliers start: 53 outliers final: 38 residues processed: 257 average time/residue: 0.3589 time to fit residues: 153.1336 Evaluate side-chains 235 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 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 B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 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 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU 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 727 THR 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 28 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 223 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 232 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.176291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118530 restraints weight = 41732.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115302 restraints weight = 27086.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115293 restraints weight = 21519.542| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25921 Z= 0.128 Angle : 0.629 12.353 35338 Z= 0.323 Chirality : 0.046 0.322 4094 Planarity : 0.004 0.046 4535 Dihedral : 5.601 58.419 4202 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 2.34 % Allowed : 9.90 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3147 helix: 1.88 (0.21), residues: 626 sheet: -0.41 (0.20), residues: 620 loop : -1.56 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 416 HIS 0.007 0.001 HIS A 232 PHE 0.033 0.001 PHE C 521 TYR 0.019 0.001 TYR B1047 ARG 0.006 0.000 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 38) link_NAG-ASN : angle 2.82662 ( 114) hydrogen bonds : bond 0.04207 ( 903) hydrogen bonds : angle 5.43126 ( 2553) covalent geometry : bond 0.00279 (25883) covalent geometry : angle 0.60958 (35224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 2.906 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 74 ASN cc_start: 0.4811 (OUTLIER) cc_final: 0.3946 (t0) REVERT: A 164 MET cc_start: 0.5825 (tpt) cc_final: 0.5186 (mmm) REVERT: A 178 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6572 (mp0) REVERT: A 371 CYS cc_start: 0.8203 (m) cc_final: 0.7878 (m) REVERT: A 380 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: A 495 PHE cc_start: 0.6088 (m-80) cc_final: 0.5478 (m-10) REVERT: B 193 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7279 (ttmm) REVERT: B 249 TYR cc_start: 0.7154 (m-80) cc_final: 0.6606 (m-80) REVERT: B 547 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: B 836 ASN cc_start: 0.8161 (m110) cc_final: 0.7882 (m110) REVERT: C 55 PHE cc_start: 0.7392 (m-80) cc_final: 0.6831 (m-10) REVERT: C 293 TYR cc_start: 0.8170 (m-80) cc_final: 0.7877 (m-80) REVERT: C 296 SER cc_start: 0.8168 (t) cc_final: 0.7852 (m) REVERT: C 297 ASN cc_start: 0.8096 (m-40) cc_final: 0.7736 (m110) REVERT: C 333 TRP cc_start: 0.5663 (p90) cc_final: 0.5363 (p90) REVERT: C 369 ASP cc_start: 0.7446 (m-30) cc_final: 0.7149 (m-30) REVERT: C 968 GLU cc_start: 0.6786 (tp30) cc_final: 0.6497 (tp30) outliers start: 65 outliers final: 46 residues processed: 258 average time/residue: 0.3450 time to fit residues: 148.4685 Evaluate side-chains 247 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 179 PHE 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 296 SER Chi-restraints excluded: chain A residue 380 PHE 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 774 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 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 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 381 VAL 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 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS B 49 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 = 0.4257 r_free = 0.4257 target = 0.175444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118355 restraints weight = 41835.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114307 restraints weight = 28393.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115139 restraints weight = 22390.338| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25921 Z= 0.147 Angle : 0.634 12.556 35338 Z= 0.325 Chirality : 0.046 0.324 4094 Planarity : 0.004 0.043 4535 Dihedral : 5.620 59.440 4202 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.20 % Rotamer: Outliers : 2.09 % Allowed : 10.44 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3147 helix: 1.86 (0.21), residues: 627 sheet: -0.44 (0.20), residues: 615 loop : -1.62 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 416 HIS 0.003 0.001 HIS B1044 PHE 0.034 0.002 PHE B 225 TYR 0.022 0.001 TYR B1047 ARG 0.005 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 38) link_NAG-ASN : angle 2.83324 ( 114) hydrogen bonds : bond 0.04250 ( 903) hydrogen bonds : angle 5.39212 ( 2553) covalent geometry : bond 0.00336 (25883) covalent geometry : angle 0.61434 (35224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5820 (tpt) cc_final: 0.5080 (mmm) REVERT: A 178 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6543 (mp0) REVERT: A 371 CYS cc_start: 0.8208 (m) cc_final: 0.7880 (m) REVERT: A 380 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4711 (m-80) REVERT: B 193 LYS cc_start: 0.7590 (ttpp) cc_final: 0.7270 (ttmm) REVERT: B 249 TYR cc_start: 0.7184 (m-80) cc_final: 0.6545 (m-80) REVERT: B 547 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7216 (mmm-85) REVERT: B 836 ASN cc_start: 0.8176 (m110) cc_final: 0.7900 (m110) REVERT: C 293 TYR cc_start: 0.8236 (m-80) cc_final: 0.7821 (m-80) REVERT: C 296 SER cc_start: 0.8147 (t) cc_final: 0.7841 (m) REVERT: C 297 ASN cc_start: 0.8088 (m-40) cc_final: 0.7713 (m110) REVERT: C 369 ASP cc_start: 0.7440 (m-30) cc_final: 0.7142 (m-30) REVERT: C 473 GLN cc_start: 0.6675 (mm-40) cc_final: 0.5804 (mt0) REVERT: C 970 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7784 (tt0) outliers start: 58 outliers final: 45 residues processed: 242 average time/residue: 0.3345 time to fit residues: 133.6552 Evaluate side-chains 238 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER 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 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 381 VAL 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 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 0.0010 chunk 106 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 12 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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 C1051 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.179797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120679 restraints weight = 41494.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119409 restraints weight = 26174.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119206 restraints weight = 19509.103| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25921 Z= 0.117 Angle : 0.612 12.121 35338 Z= 0.313 Chirality : 0.046 0.323 4094 Planarity : 0.004 0.045 4535 Dihedral : 5.456 56.972 4202 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.51 % Favored : 93.39 % Rotamer: Outliers : 1.91 % Allowed : 10.87 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3147 helix: 1.99 (0.21), residues: 625 sheet: -0.40 (0.20), residues: 583 loop : -1.60 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 416 HIS 0.003 0.000 HIS A 232 PHE 0.030 0.001 PHE C 521 TYR 0.018 0.001 TYR C1047 ARG 0.005 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 38) link_NAG-ASN : angle 2.70561 ( 114) hydrogen bonds : bond 0.03943 ( 903) hydrogen bonds : angle 5.24546 ( 2553) covalent geometry : bond 0.00247 (25883) covalent geometry : angle 0.59297 (35224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.4498 (t80) cc_final: 0.4197 (t80) REVERT: A 164 MET cc_start: 0.5777 (tpt) cc_final: 0.5018 (mmm) REVERT: A 178 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6611 (mp0) REVERT: A 371 CYS cc_start: 0.8046 (m) cc_final: 0.7750 (m) REVERT: A 380 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: A 567 ILE cc_start: 0.7802 (mt) cc_final: 0.7541 (mt) REVERT: B 193 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7282 (ttmm) REVERT: B 249 TYR cc_start: 0.7102 (m-80) cc_final: 0.6508 (m-80) REVERT: B 547 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7046 (mmm-85) REVERT: B 836 ASN cc_start: 0.8137 (m110) cc_final: 0.7866 (m110) REVERT: C 293 TYR cc_start: 0.8130 (m-80) cc_final: 0.7865 (m-80) REVERT: C 296 SER cc_start: 0.8064 (t) cc_final: 0.7779 (m) REVERT: C 297 ASN cc_start: 0.8149 (m-40) cc_final: 0.7737 (m110) REVERT: C 369 ASP cc_start: 0.7389 (m-30) cc_final: 0.7111 (m-30) REVERT: C 970 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7705 (tt0) outliers start: 53 outliers final: 44 residues processed: 249 average time/residue: 0.3336 time to fit residues: 137.0872 Evaluate side-chains 238 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 179 PHE 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 450 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 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 715 SER Chi-restraints excluded: chain B residue 759 GLN 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 1103 SER 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 218 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 182 optimal weight: 0.0570 chunk 206 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 49 HIS ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 836 ASN C1051 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.174479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121721 restraints weight = 41953.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119595 restraints weight = 38357.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120508 restraints weight = 30480.406| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.004 0.113 25921 Z= 0.171 Angle : 0.654 12.440 35338 Z= 0.334 Chirality : 0.047 0.322 4094 Planarity : 0.004 0.041 4535 Dihedral : 5.660 59.811 4202 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.88 % Rotamer: Outliers : 2.05 % Allowed : 10.83 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3147 helix: 1.78 (0.21), residues: 630 sheet: -0.52 (0.20), residues: 594 loop : -1.70 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 416 HIS 0.004 0.001 HIS B1081 PHE 0.028 0.002 PHE C 521 TYR 0.024 0.001 TYR B1047 ARG 0.008 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 38) link_NAG-ASN : angle 2.85674 ( 114) hydrogen bonds : bond 0.04367 ( 903) hydrogen bonds : angle 5.37916 ( 2553) covalent geometry : bond 0.00402 (25883) covalent geometry : angle 0.63409 (35224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5386 (tpt) cc_final: 0.4834 (mmm) REVERT: A 371 CYS cc_start: 0.7962 (m) cc_final: 0.7715 (m) REVERT: A 490 VAL cc_start: 0.6767 (OUTLIER) cc_final: 0.6495 (m) REVERT: B 193 LYS cc_start: 0.7478 (ttpp) cc_final: 0.7265 (ttmm) REVERT: B 547 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7336 (mmm-85) REVERT: B 836 ASN cc_start: 0.8056 (m110) cc_final: 0.7815 (m110) REVERT: B 963 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7753 (ttm170) REVERT: C 293 TYR cc_start: 0.8289 (m-80) cc_final: 0.7772 (m-80) REVERT: C 296 SER cc_start: 0.8123 (t) cc_final: 0.7862 (t) REVERT: C 297 ASN cc_start: 0.8030 (m-40) cc_final: 0.7731 (m110) REVERT: C 369 ASP cc_start: 0.7235 (m-30) cc_final: 0.6960 (m-30) REVERT: C 970 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7567 (tt0) outliers start: 57 outliers final: 44 residues processed: 246 average time/residue: 0.3294 time to fit residues: 133.6868 Evaluate side-chains 241 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 VAL 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 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain 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 1021 ASP Chi-restraints excluded: chain C residue 1084 VAL 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 136 optimal weight: 20.0000 chunk 215 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** 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 = 0.4246 r_free = 0.4246 target = 0.174312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114954 restraints weight = 41652.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113664 restraints weight = 27460.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112984 restraints weight = 21034.806| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 25921 Z= 0.183 Angle : 0.664 12.320 35338 Z= 0.339 Chirality : 0.047 0.326 4094 Planarity : 0.004 0.041 4535 Dihedral : 5.750 59.713 4202 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 1.91 % Allowed : 11.08 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3147 helix: 1.76 (0.21), residues: 626 sheet: -0.62 (0.20), residues: 609 loop : -1.78 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 416 HIS 0.004 0.001 HIS C1028 PHE 0.027 0.002 PHE C 521 TYR 0.025 0.002 TYR B1047 ARG 0.006 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 38) link_NAG-ASN : angle 2.91365 ( 114) hydrogen bonds : bond 0.04403 ( 903) hydrogen bonds : angle 5.42876 ( 2553) covalent geometry : bond 0.00428 (25883) covalent geometry : angle 0.64444 (35224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.4658 (t80) cc_final: 0.4423 (t80) REVERT: A 164 MET cc_start: 0.5469 (tpt) cc_final: 0.4760 (mmm) REVERT: A 371 CYS cc_start: 0.8010 (m) cc_final: 0.7755 (m) REVERT: A 544 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5875 (pt0) REVERT: B 193 LYS cc_start: 0.7533 (ttpp) cc_final: 0.7225 (ttmm) REVERT: B 547 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7011 (mmm-85) REVERT: B 836 ASN cc_start: 0.8192 (m110) cc_final: 0.7908 (m110) REVERT: B 963 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7636 (ttm170) REVERT: C 296 SER cc_start: 0.8114 (t) cc_final: 0.7857 (t) REVERT: C 297 ASN cc_start: 0.8058 (m-40) cc_final: 0.7737 (m110) REVERT: C 369 ASP cc_start: 0.7534 (m-30) cc_final: 0.7239 (m-30) REVERT: C 970 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7733 (tt0) outliers start: 53 outliers final: 47 residues processed: 239 average time/residue: 0.5571 time to fit residues: 221.1182 Evaluate side-chains 244 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER 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 264 THR 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 726 SER Chi-restraints excluded: chain C residue 800 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 230 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 228 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 257 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 194 HIS C1068 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122606 restraints weight = 41856.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121767 restraints weight = 46678.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119741 restraints weight = 35748.797| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 25921 Z= 0.263 Angle : 0.752 12.708 35338 Z= 0.382 Chirality : 0.051 0.335 4094 Planarity : 0.004 0.043 4535 Dihedral : 6.392 56.740 4202 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 1.87 % Allowed : 11.12 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3147 helix: 1.42 (0.21), residues: 628 sheet: -0.75 (0.20), residues: 605 loop : -2.03 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 866 HIS 0.008 0.001 HIS C1028 PHE 0.027 0.002 PHE C 521 TYR 0.030 0.002 TYR B1047 ARG 0.008 0.001 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 38) link_NAG-ASN : angle 3.31365 ( 114) hydrogen bonds : bond 0.05079 ( 903) hydrogen bonds : angle 5.77463 ( 2553) covalent geometry : bond 0.00627 (25883) covalent geometry : angle 0.72904 (35224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10688.50 seconds wall clock time: 189 minutes 55.10 seconds (11395.10 seconds total)