Starting phenix.real_space_refine on Thu Mar 5 18:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.map" model { file = "/net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fcd_31524/03_2026/7fcd_31524.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 110 5.16 5 C 15585 2.51 5 N 4036 2.21 5 O 4713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7901 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 13 Chain: "B" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8009 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 51, 'TRANS': 969} Chain breaks: 13 Chain: "C" Number of atoms: 8044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8044 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 52, 'TRANS': 974} Chain breaks: 12 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 5.52, per 1000 atoms: 0.23 Number of scatterers: 24444 At special positions: 0 Unit cell: (150.412, 146.021, 182.251, 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 110 16.00 O 4713 8.00 N 4036 7.00 C 15585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 657 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 370 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C1098 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 23.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.145A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.586A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.110A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.299A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.775A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.256A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.277A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 7.138A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.534A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.648A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.904A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.932A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.729A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.583A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 939 removed outlier: 4.084A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.536A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 6.130A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.544A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 4.049A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.877A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.688A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.584A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.516A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.335A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.711A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 5.193A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.520A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.864A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 5.370A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.260A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.260A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 53 removed outlier: 3.570A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.527A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.527A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.971A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 6.533A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.010A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.890A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.344A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.616A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.888A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.998A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 50 removed outlier: 4.046A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.868A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.906A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 14.898A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.461A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.906A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 14.898A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.461A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.671A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.938A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.938A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.578A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.525A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 939 hydrogen bonds defined for protein. 2574 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: 5.81 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4446 1.33 - 1.45: 6681 1.45 - 1.58: 13711 1.58 - 1.70: 2 1.70 - 1.83: 138 Bond restraints: 24978 Sorted by residual: bond pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.59e+01 bond pdb=" N ILE B 664 " pdb=" CA ILE B 664 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.14e+01 bond pdb=" CA ASP B 88 " pdb=" CB ASP B 88 " ideal model delta sigma weight residual 1.526 1.584 -0.058 1.25e-02 6.40e+03 2.14e+01 bond pdb=" N VAL B 729 " pdb=" CA VAL B 729 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.50e+01 ... (remaining 24973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 33047 2.90 - 5.79: 869 5.79 - 8.69: 36 8.69 - 11.59: 2 11.59 - 14.48: 1 Bond angle restraints: 33955 Sorted by residual: angle pdb=" N THR A 716 " pdb=" CA THR A 716 " pdb=" C THR A 716 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.31 129.91 -8.60 1.49e+00 4.50e-01 3.33e+01 angle pdb=" N THR C 716 " pdb=" CA THR C 716 " pdb=" C THR C 716 " ideal model delta sigma weight residual 114.75 107.70 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" C LEU A 293 " pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 123.65 133.79 -10.14 1.88e+00 2.83e-01 2.91e+01 angle pdb=" O PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 121.84 117.72 4.12 7.80e-01 1.64e+00 2.79e+01 ... (remaining 33950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14191 17.98 - 35.96: 952 35.96 - 53.94: 160 53.94 - 71.93: 36 71.93 - 89.91: 9 Dihedral angle restraints: 15348 sinusoidal: 6459 harmonic: 8889 Sorted by residual: dihedral pdb=" CA PHE B 329 " pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual 180.00 112.30 67.70 0 5.00e+00 4.00e-02 1.83e+02 dihedral pdb=" CA VAL B1096 " pdb=" C VAL B1096 " pdb=" N SER B1097 " pdb=" CA SER B1097 " ideal model delta harmonic sigma weight residual 180.00 116.41 63.59 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA ASN C1074 " pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta harmonic sigma weight residual 180.00 120.85 59.15 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 15345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3917 0.224 - 0.449: 40 0.449 - 0.673: 1 0.673 - 0.898: 0 0.898 - 1.122: 5 Chirality restraints: 3963 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 3960 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.362 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B1309 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.359 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG A1308 " -0.093 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.330 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1306 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.492 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.215 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 528 2.66 - 3.22: 22465 3.22 - 3.78: 37137 3.78 - 4.34: 50351 4.34 - 4.90: 80899 Nonbonded interactions: 191380 Sorted by model distance: nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.103 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.142 3.040 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.166 3.040 nonbonded pdb=" O PHE A 329 " pdb=" OG SER A 530 " model vdw 2.172 3.040 ... (remaining 191375 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 121 or resid 127 through 145 or resid 150 throu \ gh 161 or resid 164 through 170 or resid 187 through 246 or resid 259 through 34 \ 1 or resid 343 through 827 or resid 851 through 1310)) selection = (chain 'B' and (resid 14 through 17 or resid 22 through 121 or resid 127 through \ 145 or resid 150 through 170 or resid 187 through 195 or resid 200 through 246 \ or resid 259 through 341 or resid 343 through 444 or resid 447 through 617 or re \ sid 641 through 827 or resid 851 through 1310)) selection = (chain 'C' and (resid 14 through 17 or resid 22 through 121 or resid 127 through \ 145 or resid 150 through 161 or resid 164 through 170 or resid 187 through 195 \ or resid 200 through 246 or resid 259 through 444 or resid 447 through 467 or re \ sid 489 through 1310)) } 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=0.00 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: 1.970 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.910 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.009 0.087 25052 Z= 0.595 Angle : 1.168 23.783 34138 Z= 0.778 Chirality : 0.082 1.122 3963 Planarity : 0.016 0.307 4336 Dihedral : 12.310 89.908 9489 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 2.09 % Allowed : 3.36 % Favored : 94.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 2973 helix: 0.25 (0.20), residues: 626 sheet: -1.78 (0.20), residues: 614 loop : -2.64 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.024 0.002 TYR A 453 PHE 0.030 0.002 PHE C 565 TRP 0.028 0.002 TRP C 258 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00850 (24978) covalent geometry : angle 1.12649 (33955) SS BOND : bond 0.00527 ( 39) SS BOND : angle 1.32298 ( 78) hydrogen bonds : bond 0.20979 ( 884) hydrogen bonds : angle 9.12153 ( 2574) link_NAG-ASN : bond 0.02208 ( 35) link_NAG-ASN : angle 5.66188 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 166 CYS cc_start: 0.0972 (OUTLIER) cc_final: 0.0738 (t) REVERT: A 456 PHE cc_start: 0.7114 (m-10) cc_final: 0.6733 (t80) REVERT: A 509 ARG cc_start: 0.5482 (mtt180) cc_final: 0.4403 (mmt180) REVERT: B 62 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 353 TRP cc_start: 0.3838 (p-90) cc_final: 0.3340 (p-90) REVERT: B 423 TYR cc_start: 0.1134 (t80) cc_final: 0.0747 (t80) REVERT: B 822 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 878 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 172 SER cc_start: 0.0429 (OUTLIER) cc_final: -0.0005 (t) REVERT: C 374 PHE cc_start: 0.4599 (m-80) cc_final: 0.4035 (p90) REVERT: C 469 SER cc_start: 0.6463 (OUTLIER) cc_final: 0.6133 (p) REVERT: C 473 TYR cc_start: 0.5377 (m-80) cc_final: 0.5104 (m-80) REVERT: C 710 ASN cc_start: 0.7567 (p0) cc_final: 0.7302 (p0) outliers start: 56 outliers final: 8 residues processed: 203 average time/residue: 0.1493 time to fit residues: 49.4050 Evaluate side-chains 109 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 469 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 122 ASN A 125 ASN A 271 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1125 ASN B 30 ASN B 196 ASN B 370 ASN B 448 ASN B 580 GLN C 394 ASN C 690 GLN C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.106379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080219 restraints weight = 81317.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077651 restraints weight = 75316.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078093 restraints weight = 80815.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078426 restraints weight = 54375.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079142 restraints weight = 49712.539| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25052 Z= 0.163 Angle : 0.655 9.696 34138 Z= 0.334 Chirality : 0.047 0.395 3963 Planarity : 0.005 0.094 4336 Dihedral : 6.843 67.640 4009 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.35 % Rotamer: Outliers : 1.68 % Allowed : 7.09 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.15), residues: 2973 helix: 1.24 (0.21), residues: 635 sheet: -1.36 (0.20), residues: 636 loop : -2.36 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.024 0.002 TYR C1110 PHE 0.022 0.002 PHE B 168 TRP 0.020 0.002 TRP C 353 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00369 (24978) covalent geometry : angle 0.64029 (33955) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.21405 ( 78) hydrogen bonds : bond 0.05058 ( 884) hydrogen bonds : angle 6.48275 ( 2574) link_NAG-ASN : bond 0.00485 ( 35) link_NAG-ASN : angle 2.38651 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7182 (m-10) cc_final: 0.6793 (t80) REVERT: A 900 MET cc_start: 0.8852 (mtp) cc_final: 0.8616 (mtp) REVERT: B 423 TYR cc_start: 0.1258 (t80) cc_final: 0.0774 (t80) REVERT: B 822 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9082 (tp) REVERT: C 153 MET cc_start: 0.4320 (tmm) cc_final: 0.1661 (pmm) REVERT: C 400 PHE cc_start: 0.8426 (p90) cc_final: 0.7663 (p90) REVERT: C 473 TYR cc_start: 0.5843 (m-80) cc_final: 0.4983 (m-80) REVERT: C 516 GLU cc_start: 0.6472 (mp0) cc_final: 0.6250 (mp0) REVERT: C 887 THR cc_start: 0.8641 (p) cc_final: 0.8326 (t) outliers start: 45 outliers final: 22 residues processed: 163 average time/residue: 0.1547 time to fit residues: 41.1083 Evaluate side-chains 114 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 51 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 175 optimal weight: 0.0370 chunk 163 optimal weight: 9.9990 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 125 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 580 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072672 restraints weight = 82120.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.073374 restraints weight = 57918.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072874 restraints weight = 41659.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073116 restraints weight = 41214.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073219 restraints weight = 37982.303| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25052 Z= 0.205 Angle : 0.639 10.145 34138 Z= 0.328 Chirality : 0.046 0.523 3963 Planarity : 0.005 0.067 4336 Dihedral : 6.240 57.976 4002 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.60 % Allowed : 10.00 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.15), residues: 2973 helix: 1.47 (0.21), residues: 629 sheet: -1.35 (0.19), residues: 658 loop : -2.29 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.021 0.002 TYR B1067 PHE 0.018 0.002 PHE A 58 TRP 0.020 0.001 TRP C 258 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00475 (24978) covalent geometry : angle 0.62885 (33955) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.24821 ( 78) hydrogen bonds : bond 0.05031 ( 884) hydrogen bonds : angle 5.99104 ( 2574) link_NAG-ASN : bond 0.00404 ( 35) link_NAG-ASN : angle 1.96884 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7296 (t80) cc_final: 0.7095 (t80) REVERT: A 456 PHE cc_start: 0.7229 (m-10) cc_final: 0.6740 (t80) REVERT: A 516 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7249 (mt-10) REVERT: B 794 ILE cc_start: 0.8695 (mp) cc_final: 0.8199 (tp) REVERT: C 400 PHE cc_start: 0.8448 (p90) cc_final: 0.7677 (p90) REVERT: C 473 TYR cc_start: 0.6027 (m-80) cc_final: 0.5710 (m-80) REVERT: C 524 VAL cc_start: 0.6799 (OUTLIER) cc_final: 0.6544 (t) REVERT: C 887 THR cc_start: 0.8818 (p) cc_final: 0.8396 (t) outliers start: 43 outliers final: 24 residues processed: 136 average time/residue: 0.1514 time to fit residues: 33.9019 Evaluate side-chains 117 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 279 optimal weight: 0.0970 chunk 162 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 658 ASN B 901 GLN C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080680 restraints weight = 81692.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078141 restraints weight = 71634.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078764 restraints weight = 75108.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079085 restraints weight = 50381.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080595 restraints weight = 46356.248| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25052 Z= 0.105 Angle : 0.558 9.653 34138 Z= 0.282 Chirality : 0.044 0.228 3963 Planarity : 0.004 0.058 4336 Dihedral : 5.589 57.222 4000 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.60 % Allowed : 11.01 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 2973 helix: 1.97 (0.21), residues: 628 sheet: -1.23 (0.20), residues: 642 loop : -2.13 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.025 0.001 TYR A 453 PHE 0.022 0.001 PHE B 400 TRP 0.021 0.001 TRP C 258 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00229 (24978) covalent geometry : angle 0.54877 (33955) SS BOND : bond 0.00208 ( 39) SS BOND : angle 1.01410 ( 78) hydrogen bonds : bond 0.04078 ( 884) hydrogen bonds : angle 5.34911 ( 2574) link_NAG-ASN : bond 0.00433 ( 35) link_NAG-ASN : angle 1.72850 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7020 (m-10) cc_final: 0.6742 (t80) REVERT: A 900 MET cc_start: 0.8931 (mtp) cc_final: 0.8602 (mtp) REVERT: B 62 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9253 (p) REVERT: B 902 MET cc_start: 0.9000 (tpp) cc_final: 0.8781 (mmt) REVERT: C 153 MET cc_start: 0.4510 (tmm) cc_final: 0.1819 (pmm) REVERT: C 400 PHE cc_start: 0.8394 (p90) cc_final: 0.7725 (p90) REVERT: C 473 TYR cc_start: 0.6070 (m-80) cc_final: 0.5364 (m-80) REVERT: C 524 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6757 (t) outliers start: 43 outliers final: 19 residues processed: 163 average time/residue: 0.1453 time to fit residues: 39.0072 Evaluate side-chains 116 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 296 optimal weight: 4.9990 chunk 170 optimal weight: 0.0170 chunk 286 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 277 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 244 optimal weight: 0.0970 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 969 ASN C1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.106578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079992 restraints weight = 81565.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077610 restraints weight = 76034.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078337 restraints weight = 75060.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078616 restraints weight = 50998.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080204 restraints weight = 47231.511| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25052 Z= 0.121 Angle : 0.541 9.178 34138 Z= 0.275 Chirality : 0.043 0.244 3963 Planarity : 0.004 0.055 4336 Dihedral : 5.347 54.847 4000 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 12.28 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2973 helix: 2.12 (0.21), residues: 623 sheet: -1.14 (0.19), residues: 665 loop : -2.04 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.042 0.001 TYR A 453 PHE 0.020 0.001 PHE B 400 TRP 0.013 0.001 TRP C 258 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (24978) covalent geometry : angle 0.53287 (33955) SS BOND : bond 0.00196 ( 39) SS BOND : angle 0.96921 ( 78) hydrogen bonds : bond 0.03996 ( 884) hydrogen bonds : angle 5.18926 ( 2574) link_NAG-ASN : bond 0.00314 ( 35) link_NAG-ASN : angle 1.59882 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7640 (ptpt) cc_final: 0.7351 (ptpt) REVERT: A 456 PHE cc_start: 0.7058 (m-10) cc_final: 0.6797 (t80) REVERT: A 900 MET cc_start: 0.8960 (mtp) cc_final: 0.8746 (mtp) REVERT: B 62 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9249 (p) REVERT: B 990 GLU cc_start: 0.8081 (pm20) cc_final: 0.7759 (pm20) REVERT: C 28 TYR cc_start: 0.6347 (m-80) cc_final: 0.6127 (m-80) REVERT: C 400 PHE cc_start: 0.8342 (p90) cc_final: 0.7734 (p90) REVERT: C 473 TYR cc_start: 0.5959 (m-80) cc_final: 0.5747 (m-80) REVERT: C 524 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6839 (t) outliers start: 39 outliers final: 22 residues processed: 140 average time/residue: 0.1526 time to fit residues: 35.2883 Evaluate side-chains 121 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 167 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 201 optimal weight: 0.0980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.103731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070116 restraints weight = 81798.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071463 restraints weight = 55021.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071561 restraints weight = 37412.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071980 restraints weight = 32082.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072015 restraints weight = 29995.394| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25052 Z= 0.236 Angle : 0.646 10.361 34138 Z= 0.329 Chirality : 0.045 0.234 3963 Planarity : 0.005 0.073 4336 Dihedral : 5.862 57.122 4000 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 2973 helix: 1.69 (0.21), residues: 627 sheet: -1.27 (0.19), residues: 672 loop : -2.13 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.028 0.002 TYR B 904 PHE 0.020 0.002 PHE B 400 TRP 0.014 0.001 TRP C 258 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00540 (24978) covalent geometry : angle 0.63853 (33955) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.24680 ( 78) hydrogen bonds : bond 0.04835 ( 884) hydrogen bonds : angle 5.42143 ( 2574) link_NAG-ASN : bond 0.00383 ( 35) link_NAG-ASN : angle 1.64635 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7641 (ptpt) cc_final: 0.7336 (ptpt) REVERT: A 453 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6784 (p90) REVERT: A 456 PHE cc_start: 0.7256 (m-10) cc_final: 0.6775 (t80) REVERT: B 62 VAL cc_start: 0.9626 (OUTLIER) cc_final: 0.9369 (p) REVERT: B 990 GLU cc_start: 0.8114 (pm20) cc_final: 0.7748 (pm20) REVERT: C 400 PHE cc_start: 0.8445 (p90) cc_final: 0.7805 (p90) REVERT: C 473 TYR cc_start: 0.5988 (m-80) cc_final: 0.4960 (m-80) REVERT: C 524 VAL cc_start: 0.6918 (OUTLIER) cc_final: 0.6619 (t) REVERT: C 731 MET cc_start: 0.7932 (ttp) cc_final: 0.7711 (ttm) REVERT: C 751 ASN cc_start: 0.8689 (m-40) cc_final: 0.8420 (m110) REVERT: C 887 THR cc_start: 0.8840 (p) cc_final: 0.8422 (t) outliers start: 51 outliers final: 34 residues processed: 147 average time/residue: 0.1518 time to fit residues: 37.0249 Evaluate side-chains 129 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 210 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 232 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072295 restraints weight = 81468.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074006 restraints weight = 51070.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074312 restraints weight = 34170.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074673 restraints weight = 27571.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074799 restraints weight = 28439.774| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 25052 Z= 0.108 Angle : 0.555 11.928 34138 Z= 0.282 Chirality : 0.043 0.276 3963 Planarity : 0.004 0.063 4336 Dihedral : 5.420 57.415 3999 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.64 % Allowed : 13.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2973 helix: 2.13 (0.21), residues: 623 sheet: -1.08 (0.20), residues: 660 loop : -2.02 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.038 0.001 TYR A 453 PHE 0.024 0.001 PHE B 400 TRP 0.017 0.001 TRP C 258 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00244 (24978) covalent geometry : angle 0.54582 (33955) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.54223 ( 78) hydrogen bonds : bond 0.04096 ( 884) hydrogen bonds : angle 5.04044 ( 2574) link_NAG-ASN : bond 0.00300 ( 35) link_NAG-ASN : angle 1.44637 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7598 (ptpt) cc_final: 0.7286 (ptpt) REVERT: A 429 PHE cc_start: 0.7335 (t80) cc_final: 0.7126 (t80) REVERT: A 456 PHE cc_start: 0.7339 (m-10) cc_final: 0.6847 (t80) REVERT: B 62 VAL cc_start: 0.9613 (OUTLIER) cc_final: 0.9358 (p) REVERT: C 473 TYR cc_start: 0.5952 (m-80) cc_final: 0.5603 (m-80) REVERT: C 524 VAL cc_start: 0.6963 (OUTLIER) cc_final: 0.6604 (t) REVERT: C 697 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7652 (ptp) REVERT: C 751 ASN cc_start: 0.8647 (m-40) cc_final: 0.8372 (m110) REVERT: C 887 THR cc_start: 0.8794 (p) cc_final: 0.8372 (t) outliers start: 44 outliers final: 29 residues processed: 145 average time/residue: 0.1472 time to fit residues: 35.6232 Evaluate side-chains 128 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 215 optimal weight: 0.7980 chunk 276 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 139 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072011 restraints weight = 81744.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073636 restraints weight = 50902.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073918 restraints weight = 34449.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074266 restraints weight = 28459.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074386 restraints weight = 28812.889| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25052 Z= 0.123 Angle : 0.551 9.837 34138 Z= 0.280 Chirality : 0.043 0.215 3963 Planarity : 0.004 0.059 4336 Dihedral : 5.302 59.588 3999 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.57 % Allowed : 14.10 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 2973 helix: 2.10 (0.21), residues: 633 sheet: -1.04 (0.20), residues: 674 loop : -1.95 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.035 0.001 TYR A 453 PHE 0.034 0.001 PHE B 400 TRP 0.018 0.001 TRP C 258 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (24978) covalent geometry : angle 0.54458 (33955) SS BOND : bond 0.00283 ( 39) SS BOND : angle 1.12820 ( 78) hydrogen bonds : bond 0.03976 ( 884) hydrogen bonds : angle 4.91656 ( 2574) link_NAG-ASN : bond 0.00277 ( 35) link_NAG-ASN : angle 1.41373 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5325 (mtt180) cc_final: 0.4858 (mmm160) REVERT: A 386 LYS cc_start: 0.7588 (ptpt) cc_final: 0.7308 (ptpt) REVERT: A 440 ASN cc_start: 0.7229 (m110) cc_final: 0.7013 (t0) REVERT: A 456 PHE cc_start: 0.7255 (m-10) cc_final: 0.6857 (t80) REVERT: B 62 VAL cc_start: 0.9633 (OUTLIER) cc_final: 0.9371 (p) REVERT: B 122 ASN cc_start: -0.2741 (OUTLIER) cc_final: -0.3084 (m-40) REVERT: C 400 PHE cc_start: 0.8471 (p90) cc_final: 0.7900 (p90) REVERT: C 473 TYR cc_start: 0.5929 (m-80) cc_final: 0.5573 (m-80) REVERT: C 524 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6512 (t) REVERT: C 751 ASN cc_start: 0.8613 (m-40) cc_final: 0.8333 (m110) REVERT: C 887 THR cc_start: 0.8749 (p) cc_final: 0.8324 (t) outliers start: 42 outliers final: 32 residues processed: 142 average time/residue: 0.1455 time to fit residues: 34.4079 Evaluate side-chains 132 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 3 optimal weight: 0.0370 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078102 restraints weight = 81733.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076010 restraints weight = 76951.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076912 restraints weight = 82515.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076930 restraints weight = 56859.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077432 restraints weight = 48850.005| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25052 Z= 0.164 Angle : 0.582 10.112 34138 Z= 0.296 Chirality : 0.043 0.207 3963 Planarity : 0.004 0.069 4336 Dihedral : 5.528 58.522 3999 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.68 % Allowed : 14.18 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 2973 helix: 1.94 (0.21), residues: 633 sheet: -1.03 (0.19), residues: 675 loop : -1.97 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1107 TYR 0.031 0.001 TYR A 453 PHE 0.028 0.001 PHE B 400 TRP 0.018 0.001 TRP C 258 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00381 (24978) covalent geometry : angle 0.57537 (33955) SS BOND : bond 0.00286 ( 39) SS BOND : angle 1.16384 ( 78) hydrogen bonds : bond 0.04291 ( 884) hydrogen bonds : angle 5.03367 ( 2574) link_NAG-ASN : bond 0.00295 ( 35) link_NAG-ASN : angle 1.48785 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5326 (mtt180) cc_final: 0.4974 (mmm160) REVERT: A 440 ASN cc_start: 0.7411 (m110) cc_final: 0.7187 (t0) REVERT: A 456 PHE cc_start: 0.7145 (m-10) cc_final: 0.6873 (t80) REVERT: A 509 ARG cc_start: 0.4028 (mtt-85) cc_final: 0.3757 (mtt-85) REVERT: B 62 VAL cc_start: 0.9499 (OUTLIER) cc_final: 0.9268 (p) REVERT: B 122 ASN cc_start: -0.1782 (OUTLIER) cc_final: -0.2087 (m-40) REVERT: B 400 PHE cc_start: 0.2857 (p90) cc_final: 0.2101 (p90) REVERT: C 400 PHE cc_start: 0.8450 (p90) cc_final: 0.7924 (p90) REVERT: C 473 TYR cc_start: 0.5871 (m-80) cc_final: 0.5017 (m-80) REVERT: C 524 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7073 (t) REVERT: C 751 ASN cc_start: 0.8654 (m-40) cc_final: 0.8404 (m110) REVERT: C 887 THR cc_start: 0.8941 (p) cc_final: 0.8548 (t) outliers start: 45 outliers final: 37 residues processed: 147 average time/residue: 0.1434 time to fit residues: 35.7836 Evaluate side-chains 139 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 139 optimal weight: 0.0980 chunk 211 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1002 GLN B 207 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C1083 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068570 restraints weight = 81468.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069949 restraints weight = 54469.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069915 restraints weight = 38481.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070273 restraints weight = 32781.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070336 restraints weight = 30860.079| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25052 Z= 0.273 Angle : 0.712 11.670 34138 Z= 0.363 Chirality : 0.047 0.222 3963 Planarity : 0.005 0.077 4336 Dihedral : 6.662 59.015 3999 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.72 % Allowed : 14.33 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 2973 helix: 1.40 (0.21), residues: 628 sheet: -1.14 (0.20), residues: 663 loop : -2.09 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1107 TYR 0.041 0.002 TYR B 904 PHE 0.027 0.002 PHE B 400 TRP 0.016 0.002 TRP C 258 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00638 (24978) covalent geometry : angle 0.70270 (33955) SS BOND : bond 0.00402 ( 39) SS BOND : angle 1.46887 ( 78) hydrogen bonds : bond 0.05390 ( 884) hydrogen bonds : angle 5.53014 ( 2574) link_NAG-ASN : bond 0.00454 ( 35) link_NAG-ASN : angle 1.93122 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5429 (mtt180) cc_final: 0.5049 (mmm160) REVERT: A 456 PHE cc_start: 0.7095 (m-10) cc_final: 0.6795 (t80) REVERT: A 900 MET cc_start: 0.8688 (mtp) cc_final: 0.8247 (mpp) REVERT: B 62 VAL cc_start: 0.9673 (OUTLIER) cc_final: 0.9426 (p) REVERT: B 122 ASN cc_start: -0.2109 (OUTLIER) cc_final: -0.2629 (m-40) REVERT: B 400 PHE cc_start: 0.2515 (p90) cc_final: 0.1963 (p90) REVERT: C 370 ASN cc_start: 0.5776 (OUTLIER) cc_final: 0.5486 (p0) REVERT: C 392 PHE cc_start: 0.6619 (m-80) cc_final: 0.6343 (m-80) REVERT: C 400 PHE cc_start: 0.8525 (p90) cc_final: 0.7881 (p90) REVERT: C 473 TYR cc_start: 0.5465 (m-80) cc_final: 0.4489 (m-80) REVERT: C 751 ASN cc_start: 0.8655 (m-40) cc_final: 0.8394 (m110) REVERT: C 887 THR cc_start: 0.8944 (p) cc_final: 0.8561 (t) outliers start: 46 outliers final: 35 residues processed: 141 average time/residue: 0.1421 time to fit residues: 34.2962 Evaluate side-chains 129 residues out of total 2680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 133 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.103635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077201 restraints weight = 81786.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075106 restraints weight = 74938.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076017 restraints weight = 83160.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076006 restraints weight = 55141.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.076649 restraints weight = 48279.716| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 25052 Z= 0.150 Angle : 0.604 11.391 34138 Z= 0.308 Chirality : 0.044 0.225 3963 Planarity : 0.004 0.061 4336 Dihedral : 6.194 57.549 3999 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.42 % Allowed : 14.70 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 2973 helix: 1.84 (0.21), residues: 625 sheet: -1.12 (0.20), residues: 660 loop : -2.01 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.031 0.001 TYR A 453 PHE 0.027 0.001 PHE B 400 TRP 0.019 0.001 TRP C 258 HIS 0.014 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00348 (24978) covalent geometry : angle 0.59498 (33955) SS BOND : bond 0.00301 ( 39) SS BOND : angle 1.21890 ( 78) hydrogen bonds : bond 0.04558 ( 884) hydrogen bonds : angle 5.18504 ( 2574) link_NAG-ASN : bond 0.00307 ( 35) link_NAG-ASN : angle 1.71806 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.98 seconds wall clock time: 60 minutes 44.32 seconds (3644.32 seconds total)