Starting phenix.real_space_refine on Thu Mar 5 14:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7thk_25896/03_2026/7thk_25896.map" } resolution = 3.11 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= 0.081 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 104 5.16 5 C 14819 2.51 5 N 3798 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 23191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6662 Classifications: {'peptide': 860} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 40, 'TRANS': 819} Chain breaks: 9 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 8108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8108 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 990} Chain breaks: 10 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7889 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 50, 'TRANS': 971} Chain breaks: 11 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.43, per 1000 atoms: 0.23 Number of scatterers: 23191 At special positions: 0 Unit cell: (126.99, 136.95, 173.47, 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 104 16.00 O 4470 8.00 N 3798 7.00 C 14819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 131 " - pdb=" SG CYS B 166 " distance=2.04 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=1.96 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 717 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 234 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5500 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 39 sheets defined 27.4% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.295A pdb=" N TYR A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.553A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 755 removed outlier: 4.194A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.556A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.585A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 838 through 842' Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.550A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.305A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.268A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.823A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.907A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.296A pdb=" N TYR B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.661A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.081A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.832A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.668A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.707A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.165A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.664A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.157A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.912A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.866A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.296A pdb=" N TYR C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.291A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.349A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.695A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.565A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.667A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.579A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.743A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.311A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.556A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.774A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.086A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.313A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.709A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.310A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.449A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.084A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.264A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.552A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.894A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.609A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.649A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.566A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.941A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.310A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 210 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.085A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.756A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.595A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.543A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.464A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.186A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3752 1.28 - 1.42: 5957 1.42 - 1.55: 13837 1.55 - 1.69: 15 1.69 - 1.83: 131 Bond restraints: 23692 Sorted by residual: bond pdb=" C ARG B 765 " pdb=" O ARG B 765 " ideal model delta sigma weight residual 1.237 1.139 0.097 1.17e-02 7.31e+03 6.91e+01 bond pdb=" C ILE B 651 " pdb=" O ILE B 651 " ideal model delta sigma weight residual 1.238 1.165 0.072 1.09e-02 8.42e+03 4.39e+01 bond pdb=" C ILE B 693 " pdb=" O ILE B 693 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.05e-02 9.07e+03 4.01e+01 bond pdb=" C TYR B 396 " pdb=" O TYR B 396 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.20e-02 6.94e+03 3.79e+01 bond pdb=" CA SER B 359 " pdb=" CB SER B 359 " ideal model delta sigma weight residual 1.533 1.434 0.099 1.82e-02 3.02e+03 2.98e+01 ... (remaining 23687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 30364 2.83 - 5.65: 1727 5.65 - 8.48: 124 8.48 - 11.31: 9 11.31 - 14.13: 4 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C TYR B 636 " pdb=" CA TYR B 636 " pdb=" CB TYR B 636 " ideal model delta sigma weight residual 110.26 124.39 -14.13 1.50e+00 4.44e-01 8.88e+01 angle pdb=" C LYS B 278 " pdb=" CA LYS B 278 " pdb=" CB LYS B 278 " ideal model delta sigma weight residual 112.05 100.60 11.45 1.52e+00 4.33e-01 5.67e+01 angle pdb=" C CYS A 738 " pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " ideal model delta sigma weight residual 110.88 99.08 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" CA GLY C 219 " pdb=" C GLY C 219 " pdb=" O GLY C 219 " ideal model delta sigma weight residual 122.05 115.56 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA GLY B1044 " pdb=" C GLY B1044 " pdb=" O GLY B1044 " ideal model delta sigma weight residual 122.29 117.04 5.25 8.10e-01 1.52e+00 4.19e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13310 17.90 - 35.79: 1045 35.79 - 53.69: 191 53.69 - 71.59: 57 71.59 - 89.48: 15 Dihedral angle restraints: 14618 sinusoidal: 6104 harmonic: 8514 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -165.30 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.88 73.88 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.09 70.09 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 14615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2828 0.087 - 0.173: 791 0.173 - 0.260: 160 0.260 - 0.347: 29 0.347 - 0.433: 7 Chirality restraints: 3815 Sorted by residual: chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA LYS C 304 " pdb=" N LYS C 304 " pdb=" C LYS C 304 " pdb=" CB LYS C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3812 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1306 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.316 2.00e-02 2.50e+03 2.67e-01 8.91e+02 pdb=" C7 NAG C1309 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " 0.285 2.00e-02 2.50e+03 2.42e-01 7.34e+02 pdb=" C7 NAG A1311 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " 0.032 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6752 2.83 - 3.35: 19753 3.35 - 3.86: 38583 3.86 - 4.38: 45305 4.38 - 4.90: 78414 Nonbonded interactions: 188807 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.312 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.318 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.333 3.040 nonbonded pdb=" O LEU A 877 " pdb=" OG1 THR A 881 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.346 3.040 ... (remaining 188802 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 'B' and (resid 26 through 407 or (resid 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 414 or (resid 415 and (name N o \ r name CA or name C or name O or name CB )) or resid 416 through 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 442 through \ 443 or (resid 444 and (name N or name CA or name C or name O or name CB )) or r \ esid 445 through 449 or (resid 450 and (name N or name CA or name C or name O or \ name CB )) or resid 451 through 455 or (resid 456 and (name N or name CA or nam \ e C or name O or name CB )) or resid 457 through 469 or (resid 474 through 475 a \ nd (name N or name CA or name C or name O or name CB )) or resid 476 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 or (resid 500 through 501 and (name N or name CA or name C or name O or nam \ e CB )) or resid 502 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 518 or (resid 519 through 520 and ( \ name N or name CA or name C or name O or name CB )) or resid 521 through 585 or \ (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 620 or resid 641 through 827 or resid 849 through 1313)) selection = (chain 'C' and (resid 26 through 495 or (resid 496 and (name N or name CA or nam \ e C or name O or name CB )) or resid 497 through 987 or (resid 988 through 989 a \ nd (name N or name CA or name C or name O or name CB )) or resid 990 through 131 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 0.124 23766 Z= 0.648 Angle : 1.354 14.133 32414 Z= 0.932 Chirality : 0.083 0.433 3815 Planarity : 0.012 0.292 4100 Dihedral : 13.340 89.482 9010 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.44 % Allowed : 4.49 % Favored : 95.07 % Cbeta Deviations : 0.47 % 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: -1.63 (0.14), residues: 2859 helix: -1.42 (0.16), residues: 664 sheet: 0.11 (0.21), residues: 525 loop : -1.34 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 34 TYR 0.031 0.002 TYR A 37 PHE 0.045 0.003 PHE B 43 TRP 0.031 0.003 TRP B 886 HIS 0.013 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00919 (23692) covalent geometry : angle 1.33533 (32228) SS BOND : bond 0.01358 ( 36) SS BOND : angle 2.71809 ( 72) hydrogen bonds : bond 0.19594 ( 1009) hydrogen bonds : angle 8.95436 ( 2772) link_NAG-ASN : bond 0.03143 ( 38) link_NAG-ASN : angle 3.58858 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 468 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8008 (m-40) cc_final: 0.7645 (p0) REVERT: A 1031 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: B 188 ASN cc_start: 0.6454 (m-40) cc_final: 0.6014 (p0) REVERT: B 314 GLN cc_start: 0.7379 (mt0) cc_final: 0.7117 (mt0) REVERT: B 461 LEU cc_start: 0.7851 (mt) cc_final: 0.7591 (mt) REVERT: B 555 SER cc_start: 0.7161 (t) cc_final: 0.6859 (t) REVERT: B 1031 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 205 SER cc_start: 0.7697 (t) cc_final: 0.7481 (p) outliers start: 11 outliers final: 1 residues processed: 476 average time/residue: 0.1658 time to fit residues: 121.7718 Evaluate side-chains 263 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 125 ASN A 207 HIS A 544 ASN A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 542 ASN B 644 GLN B 755 GLN B 907 ASN B 914 ASN B 955 ASN C 188 ASN C 360 ASN C 710 ASN C 755 GLN C 787 GLN C 957 GLN C1005 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114096 restraints weight = 27514.435| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.39 r_work: 0.3207 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 23766 Z= 0.213 Angle : 0.662 9.888 32414 Z= 0.338 Chirality : 0.047 0.259 3815 Planarity : 0.005 0.051 4100 Dihedral : 7.290 73.729 3913 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.28 % Allowed : 9.14 % Favored : 88.58 % 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: -0.62 (0.14), residues: 2859 helix: 0.72 (0.19), residues: 665 sheet: 0.17 (0.21), residues: 559 loop : -1.12 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.024 0.002 TYR C 396 PHE 0.041 0.002 PHE B 377 TRP 0.025 0.002 TRP B 633 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00497 (23692) covalent geometry : angle 0.64056 (32228) SS BOND : bond 0.00761 ( 36) SS BOND : angle 1.69618 ( 72) hydrogen bonds : bond 0.04565 ( 1009) hydrogen bonds : angle 6.22341 ( 2772) link_NAG-ASN : bond 0.00482 ( 38) link_NAG-ASN : angle 2.57066 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6220 (OUTLIER) cc_final: 0.5394 (m-40) REVERT: A 129 LYS cc_start: 0.6930 (ttmt) cc_final: 0.6406 (tttp) REVERT: A 156 GLU cc_start: 0.5092 (pp20) cc_final: 0.4618 (mm-30) REVERT: A 271 GLN cc_start: 0.7828 (mt0) cc_final: 0.7554 (mp10) REVERT: A 613 GLN cc_start: 0.8465 (mt0) cc_final: 0.8037 (mt0) REVERT: A 990 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6769 (mp0) REVERT: B 52 GLN cc_start: 0.8325 (tt0) cc_final: 0.7709 (tm-30) REVERT: B 220 PHE cc_start: 0.7709 (t80) cc_final: 0.7498 (t80) REVERT: B 286 THR cc_start: 0.8708 (p) cc_final: 0.8331 (t) REVERT: B 314 GLN cc_start: 0.8423 (mt0) cc_final: 0.7903 (mt0) REVERT: B 378 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7238 (tttt) REVERT: B 432 CYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5997 (t) REVERT: B 740 MET cc_start: 0.8681 (mmm) cc_final: 0.8445 (tpt) REVERT: B 921 LYS cc_start: 0.8596 (mttt) cc_final: 0.7937 (ttpt) REVERT: B 1010 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8086 (mp10) REVERT: B 1031 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: C 205 SER cc_start: 0.7749 (t) cc_final: 0.7263 (p) REVERT: C 422 ASN cc_start: 0.6262 (m-40) cc_final: 0.5494 (m-40) REVERT: C 772 VAL cc_start: 0.8478 (t) cc_final: 0.8213 (m) REVERT: C 1031 GLU cc_start: 0.8671 (mm-30) cc_final: 0.7936 (mm-30) outliers start: 57 outliers final: 29 residues processed: 326 average time/residue: 0.1465 time to fit residues: 78.1794 Evaluate side-chains 271 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 122 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 265 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 258 optimal weight: 0.0980 chunk 170 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 125 ASN A 321 GLN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 417 ASN B 919 ASN B 935 GLN C 99 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.173422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113454 restraints weight = 27604.370| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.36 r_work: 0.3191 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23766 Z= 0.173 Angle : 0.592 9.497 32414 Z= 0.305 Chirality : 0.046 0.285 3815 Planarity : 0.004 0.044 4100 Dihedral : 6.718 73.055 3910 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.69 % Allowed : 9.50 % Favored : 87.82 % 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: -0.26 (0.15), residues: 2859 helix: 1.30 (0.20), residues: 685 sheet: 0.18 (0.22), residues: 536 loop : -0.96 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.002 PHE B 906 TRP 0.020 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00410 (23692) covalent geometry : angle 0.57329 (32228) SS BOND : bond 0.00436 ( 36) SS BOND : angle 1.90304 ( 72) hydrogen bonds : bond 0.04148 ( 1009) hydrogen bonds : angle 5.86309 ( 2772) link_NAG-ASN : bond 0.00327 ( 38) link_NAG-ASN : angle 2.09569 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6215 (OUTLIER) cc_final: 0.5568 (m-40) REVERT: A 129 LYS cc_start: 0.6813 (ttmt) cc_final: 0.6293 (tttp) REVERT: A 271 GLN cc_start: 0.7860 (mt0) cc_final: 0.7522 (mp10) REVERT: A 613 GLN cc_start: 0.8489 (mt0) cc_final: 0.7925 (mt0) REVERT: A 776 LYS cc_start: 0.8259 (tttt) cc_final: 0.7906 (ttpp) REVERT: A 990 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6650 (mp0) REVERT: A 1031 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 1050 MET cc_start: 0.9120 (ptp) cc_final: 0.8779 (ptm) REVERT: B 52 GLN cc_start: 0.8450 (tt0) cc_final: 0.7752 (tm-30) REVERT: B 191 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: B 220 PHE cc_start: 0.7751 (t80) cc_final: 0.7248 (t80) REVERT: B 286 THR cc_start: 0.8724 (p) cc_final: 0.8165 (t) REVERT: B 378 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7313 (tttt) REVERT: B 417 ASN cc_start: 0.7022 (t0) cc_final: 0.6697 (t0) REVERT: B 432 CYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5612 (t) REVERT: B 461 LEU cc_start: 0.7497 (mt) cc_final: 0.7266 (mt) REVERT: B 498 ARG cc_start: 0.7176 (mmt-90) cc_final: 0.6438 (mmt180) REVERT: B 572 THR cc_start: 0.7965 (p) cc_final: 0.7586 (t) REVERT: B 574 ASP cc_start: 0.7836 (t0) cc_final: 0.7589 (t0) REVERT: B 755 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8181 (mm110) REVERT: B 780 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8116 (tt0) REVERT: B 921 LYS cc_start: 0.8534 (mttt) cc_final: 0.7843 (ttpt) REVERT: B 935 GLN cc_start: 0.7470 (tt0) cc_final: 0.7247 (tt0) REVERT: B 1010 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8064 (mp10) REVERT: B 1031 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8606 (mt-10) REVERT: C 99 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 129 LYS cc_start: 0.6358 (mtpt) cc_final: 0.5666 (mtpp) REVERT: C 332 ILE cc_start: 0.8010 (pt) cc_final: 0.7802 (pt) REVERT: C 422 ASN cc_start: 0.6340 (m-40) cc_final: 0.5695 (m-40) REVERT: C 439 ASN cc_start: 0.4335 (p0) cc_final: 0.3065 (t0) REVERT: C 454 ARG cc_start: 0.6943 (ttm-80) cc_final: 0.6653 (mmm-85) REVERT: C 508 TYR cc_start: 0.5744 (m-80) cc_final: 0.4704 (m-80) REVERT: C 772 VAL cc_start: 0.8457 (t) cc_final: 0.8140 (m) REVERT: C 1031 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7820 (mm-30) outliers start: 67 outliers final: 44 residues processed: 297 average time/residue: 0.1514 time to fit residues: 72.8690 Evaluate side-chains 273 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 203 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 115 GLN A 245 HIS A 321 GLN A 613 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 370 ASN B 417 ASN B 606 ASN B 613 GLN B1101 HIS B1125 ASN C 66 HIS C 245 HIS C 710 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121019 restraints weight = 27721.840| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.47 r_work: 0.3147 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 23766 Z= 0.328 Angle : 0.709 9.456 32414 Z= 0.360 Chirality : 0.051 0.404 3815 Planarity : 0.005 0.051 4100 Dihedral : 7.175 90.932 3910 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.09 % Allowed : 11.58 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.44 (0.15), residues: 2859 helix: 1.04 (0.20), residues: 684 sheet: 0.04 (0.21), residues: 548 loop : -1.01 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.024 0.002 TYR A1067 PHE 0.030 0.002 PHE B 906 TRP 0.018 0.002 TRP B 633 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00794 (23692) covalent geometry : angle 0.68982 (32228) SS BOND : bond 0.00732 ( 36) SS BOND : angle 2.17835 ( 72) hydrogen bonds : bond 0.04930 ( 1009) hydrogen bonds : angle 6.01369 ( 2772) link_NAG-ASN : bond 0.00381 ( 38) link_NAG-ASN : angle 2.29127 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 234 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6383 (m-40) cc_final: 0.6008 (m-40) REVERT: A 129 LYS cc_start: 0.7342 (ttmt) cc_final: 0.6868 (tttm) REVERT: A 164 ASN cc_start: 0.6566 (m-40) cc_final: 0.5846 (m-40) REVERT: A 271 GLN cc_start: 0.8020 (mt0) cc_final: 0.7414 (tt0) REVERT: A 535 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7582 (mtmt) REVERT: A 541 PHE cc_start: 0.6910 (p90) cc_final: 0.6689 (p90) REVERT: A 583 GLU cc_start: 0.7198 (mp0) cc_final: 0.6949 (mp0) REVERT: A 765 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8161 (mtm-85) REVERT: A 776 LYS cc_start: 0.8683 (tttt) cc_final: 0.8270 (ttpp) REVERT: A 990 GLU cc_start: 0.7730 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 1031 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: B 317 ASN cc_start: 0.8199 (m-40) cc_final: 0.7895 (m110) REVERT: B 432 CYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6009 (t) REVERT: B 572 THR cc_start: 0.8063 (p) cc_final: 0.7724 (t) REVERT: B 574 ASP cc_start: 0.8015 (t0) cc_final: 0.7778 (t0) REVERT: B 921 LYS cc_start: 0.8761 (mttt) cc_final: 0.8227 (ttpt) REVERT: B 1005 GLN cc_start: 0.8560 (tp40) cc_final: 0.8144 (tp40) REVERT: B 1019 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: B 1031 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: C 129 LYS cc_start: 0.6873 (mtpt) cc_final: 0.5752 (mtpp) REVERT: C 140 PHE cc_start: 0.5838 (p90) cc_final: 0.5504 (p90) REVERT: C 422 ASN cc_start: 0.6362 (m-40) cc_final: 0.5830 (m-40) REVERT: C 439 ASN cc_start: 0.4399 (p0) cc_final: 0.3250 (t0) REVERT: C 454 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6399 (mmt90) REVERT: C 772 VAL cc_start: 0.8828 (t) cc_final: 0.8492 (m) REVERT: C 1031 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 77 outliers final: 51 residues processed: 294 average time/residue: 0.1412 time to fit residues: 67.3804 Evaluate side-chains 261 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 9.9990 chunk 211 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 chunk 286 optimal weight: 0.8980 chunk 96 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 314 GLN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B1125 ASN C 99 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125459 restraints weight = 27641.120| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.24 r_work: 0.3248 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23766 Z= 0.125 Angle : 0.576 14.268 32414 Z= 0.291 Chirality : 0.045 0.295 3815 Planarity : 0.004 0.047 4100 Dihedral : 6.617 75.080 3910 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.28 % Allowed : 12.91 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.12 (0.15), residues: 2859 helix: 1.59 (0.20), residues: 689 sheet: 0.18 (0.22), residues: 518 loop : -0.91 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.001 PHE C 392 TRP 0.021 0.001 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00282 (23692) covalent geometry : angle 0.55120 (32228) SS BOND : bond 0.00381 ( 36) SS BOND : angle 1.68012 ( 72) hydrogen bonds : bond 0.03682 ( 1009) hydrogen bonds : angle 5.58499 ( 2772) link_NAG-ASN : bond 0.00243 ( 38) link_NAG-ASN : angle 2.57947 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6832 (tttp) REVERT: A 164 ASN cc_start: 0.6955 (m-40) cc_final: 0.6622 (m-40) REVERT: A 271 GLN cc_start: 0.7969 (mt0) cc_final: 0.7454 (tt0) REVERT: A 541 PHE cc_start: 0.6926 (p90) cc_final: 0.6517 (p90) REVERT: A 776 LYS cc_start: 0.8579 (tttt) cc_final: 0.8167 (ttpp) REVERT: A 990 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7104 (mp0) REVERT: A 1031 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: B 132 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: B 406 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6404 (mt-10) REVERT: B 432 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.5752 (t) REVERT: B 572 THR cc_start: 0.8037 (p) cc_final: 0.7695 (t) REVERT: B 574 ASP cc_start: 0.7924 (t0) cc_final: 0.7666 (t0) REVERT: B 921 LYS cc_start: 0.8674 (mttt) cc_final: 0.8136 (ttpt) REVERT: B 1031 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: C 99 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7539 (t0) REVERT: C 140 PHE cc_start: 0.5902 (p90) cc_final: 0.5540 (p90) REVERT: C 286 THR cc_start: 0.8425 (p) cc_final: 0.8207 (p) REVERT: C 422 ASN cc_start: 0.6342 (m-40) cc_final: 0.5933 (m-40) REVERT: C 439 ASN cc_start: 0.4391 (p0) cc_final: 0.3298 (t0) REVERT: C 454 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6579 (mmt90) REVERT: C 772 VAL cc_start: 0.8689 (t) cc_final: 0.8368 (m) REVERT: C 1031 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7830 (mm-30) outliers start: 57 outliers final: 37 residues processed: 275 average time/residue: 0.1405 time to fit residues: 63.4605 Evaluate side-chains 251 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 28 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1125 ASN C 99 ASN C 955 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124583 restraints weight = 27824.305| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.29 r_work: 0.3224 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23766 Z= 0.140 Angle : 0.565 9.455 32414 Z= 0.285 Chirality : 0.045 0.260 3815 Planarity : 0.004 0.042 4100 Dihedral : 6.356 69.151 3910 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.57 % Allowed : 13.31 % Favored : 84.13 % 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: -0.02 (0.15), residues: 2859 helix: 1.79 (0.20), residues: 690 sheet: 0.08 (0.22), residues: 529 loop : -0.85 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.020 0.001 TYR A1067 PHE 0.018 0.001 PHE B 168 TRP 0.030 0.001 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (23692) covalent geometry : angle 0.54443 (32228) SS BOND : bond 0.00415 ( 36) SS BOND : angle 1.74410 ( 72) hydrogen bonds : bond 0.03652 ( 1009) hydrogen bonds : angle 5.48850 ( 2772) link_NAG-ASN : bond 0.00198 ( 38) link_NAG-ASN : angle 2.22323 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6846 (tttp) REVERT: A 164 ASN cc_start: 0.6726 (m-40) cc_final: 0.6488 (m-40) REVERT: A 271 GLN cc_start: 0.7970 (mt0) cc_final: 0.7453 (tt0) REVERT: A 776 LYS cc_start: 0.8565 (tttt) cc_final: 0.8142 (ttpp) REVERT: A 990 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7097 (mp0) REVERT: A 1031 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: B 432 CYS cc_start: 0.6652 (OUTLIER) cc_final: 0.5653 (t) REVERT: B 572 THR cc_start: 0.8074 (p) cc_final: 0.7764 (t) REVERT: B 574 ASP cc_start: 0.7930 (t0) cc_final: 0.7666 (t0) REVERT: B 580 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: B 921 LYS cc_start: 0.8678 (mttt) cc_final: 0.8133 (ttpt) REVERT: B 1125 ASN cc_start: 0.8547 (m-40) cc_final: 0.8177 (p0) REVERT: C 99 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7594 (t0) REVERT: C 121 ASN cc_start: 0.6850 (m-40) cc_final: 0.5735 (t0) REVERT: C 140 PHE cc_start: 0.5904 (p90) cc_final: 0.5542 (p90) REVERT: C 286 THR cc_start: 0.8460 (p) cc_final: 0.8250 (p) REVERT: C 388 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8846 (t0) REVERT: C 422 ASN cc_start: 0.6409 (m-40) cc_final: 0.6001 (m-40) REVERT: C 439 ASN cc_start: 0.4319 (p0) cc_final: 0.3329 (t0) REVERT: C 454 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6539 (mmt90) REVERT: C 772 VAL cc_start: 0.8657 (t) cc_final: 0.8322 (m) REVERT: C 1031 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8005 (mm-30) outliers start: 64 outliers final: 44 residues processed: 271 average time/residue: 0.1482 time to fit residues: 65.9071 Evaluate side-chains 258 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 287 optimal weight: 0.3980 chunk 188 optimal weight: 0.5980 chunk 274 optimal weight: 0.0870 chunk 291 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 125 ASN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 580 GLN B 755 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124505 restraints weight = 27735.847| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.25 r_work: 0.3228 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23766 Z= 0.140 Angle : 0.565 12.303 32414 Z= 0.286 Chirality : 0.044 0.242 3815 Planarity : 0.004 0.056 4100 Dihedral : 6.179 65.394 3907 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.48 % Allowed : 13.23 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.05 (0.15), residues: 2859 helix: 1.87 (0.20), residues: 690 sheet: 0.08 (0.21), residues: 546 loop : -0.81 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.028 0.001 TYR C 508 PHE 0.025 0.001 PHE C 65 TRP 0.030 0.001 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00329 (23692) covalent geometry : angle 0.54407 (32228) SS BOND : bond 0.00408 ( 36) SS BOND : angle 1.93433 ( 72) hydrogen bonds : bond 0.03589 ( 1009) hydrogen bonds : angle 5.40471 ( 2772) link_NAG-ASN : bond 0.00185 ( 38) link_NAG-ASN : angle 2.14592 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7318 (ttmt) cc_final: 0.6798 (tttp) REVERT: A 164 ASN cc_start: 0.7214 (m-40) cc_final: 0.6935 (m-40) REVERT: A 271 GLN cc_start: 0.8013 (mt0) cc_final: 0.7511 (tt0) REVERT: A 776 LYS cc_start: 0.8580 (tttt) cc_final: 0.8176 (ttpp) REVERT: A 990 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7117 (mp0) REVERT: A 1031 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: A 1050 MET cc_start: 0.9058 (ptp) cc_final: 0.8658 (ptm) REVERT: B 132 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6172 (mm-30) REVERT: B 572 THR cc_start: 0.8076 (p) cc_final: 0.7779 (t) REVERT: B 574 ASP cc_start: 0.7937 (t0) cc_final: 0.7671 (t0) REVERT: B 580 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: B 921 LYS cc_start: 0.8689 (mttt) cc_final: 0.8161 (ttpt) REVERT: B 1125 ASN cc_start: 0.8547 (m-40) cc_final: 0.8225 (p0) REVERT: C 121 ASN cc_start: 0.6843 (m-40) cc_final: 0.5771 (t0) REVERT: C 140 PHE cc_start: 0.5898 (p90) cc_final: 0.5534 (p90) REVERT: C 286 THR cc_start: 0.8496 (p) cc_final: 0.8295 (p) REVERT: C 388 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8844 (t0) REVERT: C 422 ASN cc_start: 0.6401 (m-40) cc_final: 0.6045 (m-40) REVERT: C 439 ASN cc_start: 0.4217 (p0) cc_final: 0.3301 (t0) REVERT: C 454 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6602 (mmt90) REVERT: C 772 VAL cc_start: 0.8654 (t) cc_final: 0.8324 (m) REVERT: C 1031 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8012 (mm-30) outliers start: 62 outliers final: 50 residues processed: 258 average time/residue: 0.1454 time to fit residues: 61.5907 Evaluate side-chains 266 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 224 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 288 optimal weight: 0.0570 chunk 234 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 overall best weight: 0.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 GLN A 125 ASN A 641 ASN B 580 GLN C 99 ASN C 955 ASN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124121 restraints weight = 27489.013| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.25 r_work: 0.3230 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23766 Z= 0.143 Angle : 0.555 9.443 32414 Z= 0.280 Chirality : 0.044 0.257 3815 Planarity : 0.004 0.050 4100 Dihedral : 6.127 62.652 3907 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.57 % Allowed : 13.11 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.07 (0.15), residues: 2859 helix: 1.91 (0.20), residues: 691 sheet: 0.08 (0.21), residues: 546 loop : -0.81 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE B 168 TRP 0.031 0.001 TRP B 633 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00337 (23692) covalent geometry : angle 0.53659 (32228) SS BOND : bond 0.00390 ( 36) SS BOND : angle 1.74849 ( 72) hydrogen bonds : bond 0.03578 ( 1009) hydrogen bonds : angle 5.36365 ( 2772) link_NAG-ASN : bond 0.00215 ( 38) link_NAG-ASN : angle 2.09381 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6750 (tttp) REVERT: A 164 ASN cc_start: 0.7229 (m-40) cc_final: 0.6968 (m-40) REVERT: A 271 GLN cc_start: 0.7982 (mt0) cc_final: 0.7430 (tt0) REVERT: A 776 LYS cc_start: 0.8557 (tttt) cc_final: 0.8138 (ttpp) REVERT: A 990 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7117 (mp0) REVERT: A 1031 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: A 1050 MET cc_start: 0.9074 (ptp) cc_final: 0.8670 (ptm) REVERT: B 132 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6178 (mm-30) REVERT: B 188 ASN cc_start: 0.5522 (m-40) cc_final: 0.5003 (t0) REVERT: B 331 ASN cc_start: 0.6646 (m-40) cc_final: 0.6376 (m-40) REVERT: B 572 THR cc_start: 0.8034 (p) cc_final: 0.7749 (t) REVERT: B 574 ASP cc_start: 0.7889 (t0) cc_final: 0.7663 (t0) REVERT: B 755 GLN cc_start: 0.8806 (mm110) cc_final: 0.8604 (mm110) REVERT: B 921 LYS cc_start: 0.8678 (mttt) cc_final: 0.8127 (ttpt) REVERT: B 934 ILE cc_start: 0.8674 (tt) cc_final: 0.8352 (tt) REVERT: B 1125 ASN cc_start: 0.8516 (m-40) cc_final: 0.8199 (p0) REVERT: C 99 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7475 (t0) REVERT: C 121 ASN cc_start: 0.6886 (m-40) cc_final: 0.5825 (t0) REVERT: C 140 PHE cc_start: 0.5868 (p90) cc_final: 0.5505 (p90) REVERT: C 294 ASP cc_start: 0.7863 (m-30) cc_final: 0.7660 (t0) REVERT: C 388 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8839 (t0) REVERT: C 422 ASN cc_start: 0.6365 (m-40) cc_final: 0.6034 (m-40) REVERT: C 439 ASN cc_start: 0.4162 (p0) cc_final: 0.3284 (t0) REVERT: C 454 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6651 (mmt90) REVERT: C 555 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (p) REVERT: C 772 VAL cc_start: 0.8648 (t) cc_final: 0.8294 (m) REVERT: C 1031 GLU cc_start: 0.8615 (mm-30) cc_final: 0.7979 (mm-30) outliers start: 64 outliers final: 54 residues processed: 263 average time/residue: 0.1312 time to fit residues: 57.0926 Evaluate side-chains 267 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 165 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 257 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 246 optimal weight: 0.0170 chunk 135 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 99 ASN A 125 ASN A 641 ASN C 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125017 restraints weight = 27656.172| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.26 r_work: 0.3247 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23766 Z= 0.125 Angle : 0.552 9.498 32414 Z= 0.280 Chirality : 0.044 0.273 3815 Planarity : 0.004 0.047 4100 Dihedral : 6.052 58.513 3907 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.36 % Allowed : 13.51 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.14 (0.15), residues: 2859 helix: 1.98 (0.20), residues: 696 sheet: 0.14 (0.21), residues: 555 loop : -0.79 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.020 0.001 TYR A1067 PHE 0.018 0.001 PHE B 220 TRP 0.033 0.001 TRP B 633 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00291 (23692) covalent geometry : angle 0.53296 (32228) SS BOND : bond 0.00383 ( 36) SS BOND : angle 1.85020 ( 72) hydrogen bonds : bond 0.03474 ( 1009) hydrogen bonds : angle 5.31025 ( 2772) link_NAG-ASN : bond 0.00192 ( 38) link_NAG-ASN : angle 2.05171 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7321 (ttmt) cc_final: 0.6740 (tttp) REVERT: A 164 ASN cc_start: 0.7348 (m-40) cc_final: 0.7092 (m-40) REVERT: A 271 GLN cc_start: 0.7955 (mt0) cc_final: 0.7408 (tt0) REVERT: A 776 LYS cc_start: 0.8550 (tttt) cc_final: 0.8140 (ttpp) REVERT: A 990 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7111 (mp0) REVERT: A 1031 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8641 (mt-10) REVERT: A 1050 MET cc_start: 0.9067 (ptp) cc_final: 0.8681 (ptm) REVERT: B 132 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: B 188 ASN cc_start: 0.5456 (m-40) cc_final: 0.4679 (t0) REVERT: B 572 THR cc_start: 0.8094 (p) cc_final: 0.7790 (t) REVERT: B 921 LYS cc_start: 0.8672 (mttt) cc_final: 0.8142 (ttpt) REVERT: B 934 ILE cc_start: 0.8668 (tt) cc_final: 0.8354 (tt) REVERT: B 1125 ASN cc_start: 0.8507 (m-40) cc_final: 0.8256 (p0) REVERT: C 99 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7600 (t0) REVERT: C 121 ASN cc_start: 0.6855 (m-40) cc_final: 0.5835 (t0) REVERT: C 140 PHE cc_start: 0.5843 (p90) cc_final: 0.5478 (p90) REVERT: C 294 ASP cc_start: 0.7818 (m-30) cc_final: 0.7617 (t0) REVERT: C 388 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8844 (t0) REVERT: C 422 ASN cc_start: 0.6367 (m-40) cc_final: 0.6039 (m-40) REVERT: C 439 ASN cc_start: 0.4100 (p0) cc_final: 0.3226 (t0) REVERT: C 454 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6657 (mmt90) REVERT: C 555 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8194 (p) REVERT: C 772 VAL cc_start: 0.8630 (t) cc_final: 0.8277 (m) REVERT: C 1031 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8095 (mp0) outliers start: 59 outliers final: 51 residues processed: 258 average time/residue: 0.1473 time to fit residues: 62.5224 Evaluate side-chains 264 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 225 optimal weight: 0.8980 chunk 233 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 234 optimal weight: 0.0020 chunk 266 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 126 optimal weight: 0.0070 chunk 113 optimal weight: 0.9990 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 641 ASN B 580 GLN C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.176894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125715 restraints weight = 27667.288| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3261 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23766 Z= 0.115 Angle : 0.543 9.467 32414 Z= 0.275 Chirality : 0.044 0.283 3815 Planarity : 0.004 0.046 4100 Dihedral : 5.958 56.037 3907 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.08 % Allowed : 13.99 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.24 (0.15), residues: 2859 helix: 2.09 (0.20), residues: 694 sheet: 0.24 (0.21), residues: 544 loop : -0.74 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.020 0.001 TYR A1067 PHE 0.035 0.001 PHE B 168 TRP 0.033 0.001 TRP B 633 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00264 (23692) covalent geometry : angle 0.52454 (32228) SS BOND : bond 0.00354 ( 36) SS BOND : angle 1.59747 ( 72) hydrogen bonds : bond 0.03371 ( 1009) hydrogen bonds : angle 5.23713 ( 2772) link_NAG-ASN : bond 0.00178 ( 38) link_NAG-ASN : angle 2.13878 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8110 (m-10) cc_final: 0.7819 (m-10) REVERT: A 129 LYS cc_start: 0.7260 (ttmt) cc_final: 0.6662 (tttp) REVERT: A 156 GLU cc_start: 0.4964 (pp20) cc_final: 0.4528 (mm-30) REVERT: A 164 ASN cc_start: 0.7354 (m-40) cc_final: 0.7076 (m-40) REVERT: A 271 GLN cc_start: 0.7994 (mt0) cc_final: 0.7445 (tt0) REVERT: A 776 LYS cc_start: 0.8536 (tttt) cc_final: 0.8138 (ttpp) REVERT: A 990 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7116 (mp0) REVERT: A 1031 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: A 1050 MET cc_start: 0.9053 (ptp) cc_final: 0.8653 (ptm) REVERT: B 132 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: B 188 ASN cc_start: 0.5357 (m-40) cc_final: 0.4892 (t0) REVERT: B 378 LYS cc_start: 0.7880 (tttt) cc_final: 0.7254 (tptt) REVERT: B 572 THR cc_start: 0.8100 (p) cc_final: 0.7790 (t) REVERT: B 921 LYS cc_start: 0.8660 (mttt) cc_final: 0.8132 (ttpt) REVERT: B 934 ILE cc_start: 0.8633 (tt) cc_final: 0.8343 (tt) REVERT: B 1125 ASN cc_start: 0.8481 (m-40) cc_final: 0.8244 (p0) REVERT: C 121 ASN cc_start: 0.6797 (m-40) cc_final: 0.5896 (t0) REVERT: C 140 PHE cc_start: 0.5848 (p90) cc_final: 0.5481 (p90) REVERT: C 388 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8824 (t0) REVERT: C 422 ASN cc_start: 0.6527 (m-40) cc_final: 0.6157 (m-40) REVERT: C 439 ASN cc_start: 0.4101 (p0) cc_final: 0.3222 (t0) REVERT: C 454 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6686 (mmt90) REVERT: C 555 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8198 (p) REVERT: C 772 VAL cc_start: 0.8608 (t) cc_final: 0.8232 (m) REVERT: C 1031 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8031 (mm-30) outliers start: 52 outliers final: 45 residues processed: 251 average time/residue: 0.1474 time to fit residues: 60.6205 Evaluate side-chains 255 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 74 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 235 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 230 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 252 optimal weight: 0.0370 chunk 274 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.177055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125910 restraints weight = 27548.822| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.26 r_work: 0.3267 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23766 Z= 0.118 Angle : 0.534 9.484 32414 Z= 0.271 Chirality : 0.044 0.296 3815 Planarity : 0.004 0.045 4100 Dihedral : 5.854 56.433 3907 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.24 % Allowed : 13.59 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.15), residues: 2859 helix: 2.16 (0.20), residues: 693 sheet: 0.26 (0.21), residues: 583 loop : -0.67 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.033 0.001 TYR B 170 PHE 0.015 0.001 PHE A 168 TRP 0.023 0.001 TRP B 633 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00273 (23692) covalent geometry : angle 0.51804 (32228) SS BOND : bond 0.00351 ( 36) SS BOND : angle 1.49561 ( 72) hydrogen bonds : bond 0.03338 ( 1009) hydrogen bonds : angle 5.17998 ( 2772) link_NAG-ASN : bond 0.00170 ( 38) link_NAG-ASN : angle 1.95880 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.19 seconds wall clock time: 126 minutes 57.83 seconds (7617.83 seconds total)