Starting phenix.real_space_refine on Fri Jun 20 02:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_25896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_25896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_25896.map" model { file = "/net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_25896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7thk_25896/06_2025/7thk_25896.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.081 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP: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: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} 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: 14.50, per 1000 atoms: 0.63 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: 5.39 Conformation dependent library (CDL) restraints added in 2.7 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: 2.93 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: 10.56 Time building geometry restraints manager: 6.26 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 1147 or resid 1301 th \ rough 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 114 \ 7 or resid 1301 through 1313)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.280 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (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 TRP 0.031 0.003 TRP B 886 HIS 0.013 0.001 HIS A 954 PHE 0.045 0.003 PHE B 43 TYR 0.031 0.002 TYR A 37 ARG 0.010 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.03143 ( 38) link_NAG-ASN : angle 3.58858 ( 114) hydrogen bonds : bond 0.19594 ( 1009) hydrogen bonds : angle 8.95436 ( 2772) SS BOND : bond 0.01358 ( 36) SS BOND : angle 2.71809 ( 72) covalent geometry : bond 0.00919 (23692) covalent geometry : angle 1.33533 (32228) *********************** 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 : 2.467 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: 0.7644 (p0) REVERT: A 740 MET cc_start: 0.7291 (tpt) cc_final: 0.6927 (tpt) REVERT: A 1031 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: B 188 ASN cc_start: 0.6454 (m-40) cc_final: 0.6013 (p0) REVERT: B 314 GLN cc_start: 0.7379 (mt0) cc_final: 0.7120 (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: 0.6856 (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: 0.7480 (p) outliers start: 11 outliers final: 1 residues processed: 476 average time/residue: 0.3944 time to fit residues: 292.8361 Evaluate side-chains 265 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 246 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 321 GLN 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 606 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 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116149 restraints weight = 27431.276| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.36 r_work: 0.3230 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23766 Z= 0.178 Angle : 0.636 10.323 32414 Z= 0.326 Chirality : 0.046 0.281 3815 Planarity : 0.004 0.050 4100 Dihedral : 7.177 69.884 3913 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.04 % Allowed : 9.10 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 2859 helix: 0.80 (0.19), residues: 659 sheet: 0.19 (0.21), residues: 567 loop : -1.09 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.040 0.002 PHE B 377 TYR 0.019 0.002 TYR C 396 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 38) link_NAG-ASN : angle 2.49095 ( 114) hydrogen bonds : bond 0.04416 ( 1009) hydrogen bonds : angle 6.18376 ( 2772) SS BOND : bond 0.00475 ( 36) SS BOND : angle 1.61608 ( 72) covalent geometry : bond 0.00412 (23692) covalent geometry : angle 0.61538 (32228) *********************** 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 335 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7398 (t0) REVERT: A 125 ASN cc_start: 0.6182 (OUTLIER) cc_final: 0.5393 (m-40) REVERT: A 129 LYS cc_start: 0.6922 (ttmt) cc_final: 0.6409 (tttp) REVERT: A 156 GLU cc_start: 0.5050 (pp20) cc_final: 0.4589 (mm-30) REVERT: A 190 ARG cc_start: 0.7384 (mtp180) cc_final: 0.7030 (mtt180) REVERT: A 271 GLN cc_start: 0.7839 (mt0) cc_final: 0.7573 (mp10) REVERT: A 613 GLN cc_start: 0.8426 (mt0) cc_final: 0.7979 (mt0) REVERT: A 990 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6770 (mp0) REVERT: B 52 GLN cc_start: 0.8308 (tt0) cc_final: 0.7722 (tm-30) REVERT: B 286 THR cc_start: 0.8689 (p) cc_final: 0.8296 (t) REVERT: B 314 GLN cc_start: 0.8377 (mt0) cc_final: 0.7858 (mt0) REVERT: B 378 LYS cc_start: 0.7589 (mtpt) cc_final: 0.7342 (tttt) REVERT: B 432 CYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6044 (t) REVERT: B 516 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: B 740 MET cc_start: 0.8679 (mmm) cc_final: 0.8438 (tpt) REVERT: B 921 LYS cc_start: 0.8614 (mttt) cc_final: 0.7962 (ttpt) REVERT: B 1010 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8056 (mp10) REVERT: B 1031 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: C 129 LYS cc_start: 0.6553 (tttt) cc_final: 0.6348 (tttt) REVERT: C 205 SER cc_start: 0.7699 (t) cc_final: 0.7204 (p) REVERT: C 422 ASN cc_start: 0.6324 (m-40) cc_final: 0.5538 (m-40) REVERT: C 772 VAL cc_start: 0.8398 (t) cc_final: 0.8162 (m) REVERT: C 1031 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7916 (mm-30) outliers start: 51 outliers final: 23 residues processed: 321 average time/residue: 0.3661 time to fit residues: 191.1460 Evaluate side-chains 264 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 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 919 ASN Chi-restraints excluded: chain A residue 1031 GLU 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 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 516 GLU 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 1031 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 708 SER 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 220 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 216 optimal weight: 0.0050 chunk 286 optimal weight: 0.3980 chunk 179 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 613 GLN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 755 GLN B 919 ASN B 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116104 restraints weight = 27393.878| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.38 r_work: 0.3230 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23766 Z= 0.128 Angle : 0.557 9.517 32414 Z= 0.287 Chirality : 0.044 0.283 3815 Planarity : 0.004 0.046 4100 Dihedral : 6.542 64.256 3910 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 9.78 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2859 helix: 1.49 (0.19), residues: 685 sheet: 0.24 (0.22), residues: 562 loop : -0.95 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 633 HIS 0.003 0.001 HIS A1048 PHE 0.017 0.001 PHE B 906 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 38) link_NAG-ASN : angle 2.03293 ( 114) hydrogen bonds : bond 0.03862 ( 1009) hydrogen bonds : angle 5.77405 ( 2772) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.78755 ( 72) covalent geometry : bond 0.00291 (23692) covalent geometry : angle 0.53834 (32228) *********************** 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 312 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7837 (t0) cc_final: 0.7399 (t0) REVERT: A 125 ASN cc_start: 0.6115 (OUTLIER) cc_final: 0.5437 (m-40) REVERT: A 129 LYS cc_start: 0.6995 (ttmt) cc_final: 0.6459 (tttp) REVERT: A 271 GLN cc_start: 0.7816 (mt0) cc_final: 0.7549 (mp10) REVERT: A 613 GLN cc_start: 0.8491 (mt0) cc_final: 0.7992 (mt0) REVERT: A 776 LYS cc_start: 0.8336 (tttt) cc_final: 0.8023 (ttpp) REVERT: A 990 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6750 (mp0) REVERT: A 1031 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: A 1119 ASN cc_start: 0.7430 (m-40) cc_final: 0.7065 (m-40) REVERT: B 52 GLN cc_start: 0.8358 (tt0) cc_final: 0.7757 (tm-30) REVERT: B 314 GLN cc_start: 0.8325 (mt0) cc_final: 0.7872 (mt0) REVERT: B 378 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7422 (tttt) REVERT: B 417 ASN cc_start: 0.7008 (t0) cc_final: 0.6718 (t0) REVERT: B 432 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5685 (t) REVERT: B 461 LEU cc_start: 0.7464 (mt) cc_final: 0.7183 (mt) REVERT: B 498 ARG cc_start: 0.7144 (mmt-90) cc_final: 0.6415 (mmt180) REVERT: B 516 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: B 572 THR cc_start: 0.8072 (p) cc_final: 0.7660 (t) REVERT: B 574 ASP cc_start: 0.7874 (t0) cc_final: 0.7646 (t0) REVERT: B 580 GLN cc_start: 0.8266 (mt0) cc_final: 0.7945 (mm-40) REVERT: B 755 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8019 (mm-40) REVERT: B 921 LYS cc_start: 0.8570 (mttt) cc_final: 0.7951 (ttpt) REVERT: B 935 GLN cc_start: 0.7577 (tt0) cc_final: 0.7252 (tt0) REVERT: B 1010 GLN cc_start: 0.8254 (mm-40) cc_final: 0.8032 (mp10) REVERT: B 1031 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: C 190 ARG cc_start: 0.7307 (mtm-85) cc_final: 0.6891 (ptp-110) REVERT: C 422 ASN cc_start: 0.6371 (m-40) cc_final: 0.5635 (m-40) REVERT: C 439 ASN cc_start: 0.4372 (p0) cc_final: 0.3071 (t0) REVERT: C 454 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6593 (mmm-85) REVERT: C 508 TYR cc_start: 0.5841 (m-80) cc_final: 0.4785 (m-80) REVERT: C 772 VAL cc_start: 0.8419 (t) cc_final: 0.8133 (m) REVERT: C 1031 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8194 (mp0) outliers start: 61 outliers final: 44 residues processed: 295 average time/residue: 0.3423 time to fit residues: 163.9023 Evaluate side-chains 279 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 240 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 919 ASN 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 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 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 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU 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 794 ILE 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 C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 189 LEU 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 1072 GLU 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 227 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 321 GLN A 641 ASN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 370 ASN B 417 ASN B1101 HIS C 99 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.170687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109847 restraints weight = 27713.635| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.60 r_work: 0.3128 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 23766 Z= 0.238 Angle : 0.628 9.495 32414 Z= 0.320 Chirality : 0.047 0.277 3815 Planarity : 0.004 0.040 4100 Dihedral : 6.669 74.869 3910 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 10.46 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2859 helix: 1.37 (0.20), residues: 686 sheet: 0.22 (0.22), residues: 552 loop : -0.88 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 633 HIS 0.006 0.001 HIS A1048 PHE 0.029 0.002 PHE B 906 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 38) link_NAG-ASN : angle 2.09190 ( 114) hydrogen bonds : bond 0.04400 ( 1009) hydrogen bonds : angle 5.81947 ( 2772) SS BOND : bond 0.00574 ( 36) SS BOND : angle 1.96305 ( 72) covalent geometry : bond 0.00572 (23692) covalent geometry : angle 0.60991 (32228) *********************** 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 318 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6285 (m-40) cc_final: 0.6052 (m-40) REVERT: A 129 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6511 (tttm) REVERT: A 271 GLN cc_start: 0.7961 (mt0) cc_final: 0.7624 (mp10) REVERT: A 541 PHE cc_start: 0.6781 (p90) cc_final: 0.6526 (p90) REVERT: A 776 LYS cc_start: 0.8428 (tttt) cc_final: 0.7984 (ttpp) REVERT: A 912 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8911 (p) REVERT: A 990 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6764 (mp0) REVERT: A 1031 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8655 (mt-10) REVERT: A 1050 MET cc_start: 0.9226 (ptp) cc_final: 0.8929 (ptm) REVERT: B 52 GLN cc_start: 0.8500 (tt0) cc_final: 0.7777 (tm-30) REVERT: B 96 GLU cc_start: 0.6546 (pm20) cc_final: 0.6253 (pm20) REVERT: B 432 CYS cc_start: 0.6691 (OUTLIER) cc_final: 0.5725 (t) REVERT: B 498 ARG cc_start: 0.7296 (mmt-90) cc_final: 0.6360 (mmt180) REVERT: B 572 THR cc_start: 0.8001 (p) cc_final: 0.7660 (t) REVERT: B 574 ASP cc_start: 0.7967 (t0) cc_final: 0.7728 (t0) REVERT: B 914 ASN cc_start: 0.9083 (p0) cc_final: 0.8877 (p0) REVERT: B 921 LYS cc_start: 0.8617 (mttt) cc_final: 0.7981 (ttpt) REVERT: B 935 GLN cc_start: 0.7605 (tt0) cc_final: 0.7374 (tt0) REVERT: B 1019 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7848 (ttp80) REVERT: C 99 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7300 (t0) REVERT: C 140 PHE cc_start: 0.5752 (p90) cc_final: 0.5375 (p90) REVERT: C 422 ASN cc_start: 0.6363 (m-40) cc_final: 0.5759 (m-40) REVERT: C 439 ASN cc_start: 0.4210 (p0) cc_final: 0.3031 (t0) REVERT: C 454 ARG cc_start: 0.6930 (ttm-80) cc_final: 0.6281 (mmt90) REVERT: C 508 TYR cc_start: 0.5667 (m-80) cc_final: 0.4619 (m-80) REVERT: C 772 VAL cc_start: 0.8595 (t) cc_final: 0.8236 (m) REVERT: C 983 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7423 (mtp-110) REVERT: C 1031 GLU cc_start: 0.8851 (mm-30) cc_final: 0.7831 (mm-30) outliers start: 72 outliers final: 50 residues processed: 299 average time/residue: 0.3859 time to fit residues: 194.2751 Evaluate side-chains 271 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 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 912 THR 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 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 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 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 724 THR Chi-restraints excluded: chain B residue 791 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 C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 85 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 286 optimal weight: 0.0970 chunk 221 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 613 GLN B 755 GLN B1125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112724 restraints weight = 27418.377| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.49 r_work: 0.3175 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23766 Z= 0.137 Angle : 0.548 9.436 32414 Z= 0.281 Chirality : 0.044 0.248 3815 Planarity : 0.004 0.040 4100 Dihedral : 6.204 68.366 3907 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.32 % Allowed : 12.22 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.15), residues: 2859 helix: 1.69 (0.20), residues: 693 sheet: 0.23 (0.22), residues: 530 loop : -0.84 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 633 HIS 0.003 0.001 HIS A1048 PHE 0.023 0.001 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 38) link_NAG-ASN : angle 1.89490 ( 114) hydrogen bonds : bond 0.03698 ( 1009) hydrogen bonds : angle 5.54328 ( 2772) SS BOND : bond 0.00378 ( 36) SS BOND : angle 1.62587 ( 72) covalent geometry : bond 0.00321 (23692) covalent geometry : angle 0.53257 (32228) *********************** 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 291 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6565 (tttp) REVERT: A 164 ASN cc_start: 0.6647 (m-40) cc_final: 0.6319 (m-40) REVERT: A 271 GLN cc_start: 0.7928 (mt0) cc_final: 0.7374 (tt0) REVERT: A 541 PHE cc_start: 0.6799 (p90) cc_final: 0.6407 (p90) REVERT: A 776 LYS cc_start: 0.8364 (tttt) cc_final: 0.7899 (ttpp) REVERT: A 990 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6812 (mp0) REVERT: A 1031 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: A 1050 MET cc_start: 0.9193 (ptp) cc_final: 0.8931 (ptm) REVERT: B 52 GLN cc_start: 0.8482 (tt0) cc_final: 0.7819 (tm-30) REVERT: B 96 GLU cc_start: 0.6432 (pm20) cc_final: 0.6192 (pm20) REVERT: B 132 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: B 432 CYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5574 (t) REVERT: B 498 ARG cc_start: 0.7319 (mmt-90) cc_final: 0.6454 (mmt180) REVERT: B 572 THR cc_start: 0.7919 (p) cc_final: 0.7606 (t) REVERT: B 574 ASP cc_start: 0.7901 (t0) cc_final: 0.7650 (t0) REVERT: B 580 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: B 633 TRP cc_start: 0.7690 (p-90) cc_final: 0.7485 (p-90) REVERT: B 921 LYS cc_start: 0.8571 (mttt) cc_final: 0.7925 (ttpt) REVERT: B 1019 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7793 (ttp80) REVERT: C 129 LYS cc_start: 0.6374 (mtpt) cc_final: 0.5887 (mtpt) REVERT: C 140 PHE cc_start: 0.5750 (p90) cc_final: 0.5373 (p90) REVERT: C 286 THR cc_start: 0.8304 (p) cc_final: 0.8086 (p) REVERT: C 422 ASN cc_start: 0.6289 (m-40) cc_final: 0.5821 (m-40) REVERT: C 439 ASN cc_start: 0.4378 (p0) cc_final: 0.3273 (t0) REVERT: C 454 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6556 (mmt90) REVERT: C 508 TYR cc_start: 0.5677 (m-80) cc_final: 0.4584 (m-80) REVERT: C 574 ASP cc_start: 0.8294 (t0) cc_final: 0.7899 (t0) REVERT: C 772 VAL cc_start: 0.8507 (t) cc_final: 0.8154 (m) REVERT: C 983 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7528 (mtp-110) REVERT: C 1031 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7951 (mm-30) outliers start: 58 outliers final: 43 residues processed: 275 average time/residue: 0.3200 time to fit residues: 143.5715 Evaluate side-chains 266 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 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 627 ASP 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 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 393 THR Chi-restraints excluded: chain B residue 407 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 724 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 80 ASP 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 511 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 188 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 115 GLN A 125 ASN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 755 GLN B1125 ASN C 804 GLN C 955 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112359 restraints weight = 27212.331| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.53 r_work: 0.3164 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23766 Z= 0.142 Angle : 0.545 9.458 32414 Z= 0.279 Chirality : 0.044 0.259 3815 Planarity : 0.004 0.042 4100 Dihedral : 6.067 65.933 3907 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.48 % Allowed : 12.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2859 helix: 1.82 (0.20), residues: 695 sheet: 0.24 (0.22), residues: 528 loop : -0.81 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 633 HIS 0.003 0.001 HIS A1048 PHE 0.024 0.001 PHE C 65 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 38) link_NAG-ASN : angle 1.81072 ( 114) hydrogen bonds : bond 0.03671 ( 1009) hydrogen bonds : angle 5.45171 ( 2772) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.79433 ( 72) covalent geometry : bond 0.00336 (23692) covalent geometry : angle 0.52881 (32228) *********************** 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 287 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7114 (ttmt) cc_final: 0.6674 (tttp) REVERT: A 271 GLN cc_start: 0.7955 (mt0) cc_final: 0.7415 (tt0) REVERT: A 541 PHE cc_start: 0.6851 (p90) cc_final: 0.6486 (p90) REVERT: A 560 LEU cc_start: 0.8036 (mt) cc_final: 0.7835 (mt) REVERT: A 583 GLU cc_start: 0.7114 (mp0) cc_final: 0.6900 (mp0) REVERT: A 776 LYS cc_start: 0.8419 (tttt) cc_final: 0.7982 (ttpp) REVERT: A 990 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6988 (mp0) REVERT: A 1031 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: A 1050 MET cc_start: 0.9179 (ptp) cc_final: 0.8909 (ptm) REVERT: B 96 GLU cc_start: 0.6519 (pm20) cc_final: 0.6253 (pm20) REVERT: B 226 LEU cc_start: 0.8074 (tt) cc_final: 0.7816 (tt) REVERT: B 432 CYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5547 (t) REVERT: B 572 THR cc_start: 0.8030 (p) cc_final: 0.7728 (t) REVERT: B 574 ASP cc_start: 0.7934 (t0) cc_final: 0.7684 (t0) REVERT: B 580 GLN cc_start: 0.8481 (mt0) cc_final: 0.8225 (mm-40) REVERT: B 921 LYS cc_start: 0.8617 (mttt) cc_final: 0.7990 (ttpt) REVERT: B 1019 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7868 (ttp80) REVERT: B 1031 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8722 (mt-10) REVERT: C 129 LYS cc_start: 0.6541 (mtpt) cc_final: 0.5997 (mtpt) REVERT: C 140 PHE cc_start: 0.5758 (p90) cc_final: 0.5381 (p90) REVERT: C 286 THR cc_start: 0.8366 (p) cc_final: 0.8137 (p) REVERT: C 422 ASN cc_start: 0.6285 (m-40) cc_final: 0.5860 (m-40) REVERT: C 439 ASN cc_start: 0.4360 (p0) cc_final: 0.3260 (t0) REVERT: C 454 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6539 (mmt90) REVERT: C 508 TYR cc_start: 0.5727 (m-80) cc_final: 0.4617 (m-80) REVERT: C 574 ASP cc_start: 0.8325 (t0) cc_final: 0.7961 (t0) REVERT: C 772 VAL cc_start: 0.8554 (t) cc_final: 0.8190 (m) REVERT: C 983 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7595 (mtp-110) REVERT: C 1031 GLU cc_start: 0.8734 (mm-30) cc_final: 0.7927 (mm-30) outliers start: 62 outliers final: 48 residues processed: 274 average time/residue: 0.3138 time to fit residues: 140.1476 Evaluate side-chains 271 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 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 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 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 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 393 THR Chi-restraints excluded: chain B residue 407 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 724 THR Chi-restraints excluded: chain B residue 791 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 80 ASP 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 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 44 optimal weight: 0.6980 chunk 235 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 125 ASN A 245 HIS A 804 GLN A 935 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1125 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111117 restraints weight = 27380.929| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.61 r_work: 0.3147 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23766 Z= 0.168 Angle : 0.566 11.872 32414 Z= 0.290 Chirality : 0.045 0.241 3815 Planarity : 0.004 0.048 4100 Dihedral : 6.087 66.232 3907 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.65 % Allowed : 12.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2859 helix: 1.79 (0.20), residues: 696 sheet: 0.18 (0.21), residues: 579 loop : -0.77 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 38) link_NAG-ASN : angle 1.86824 ( 114) hydrogen bonds : bond 0.03759 ( 1009) hydrogen bonds : angle 5.43771 ( 2772) SS BOND : bond 0.00383 ( 36) SS BOND : angle 2.04558 ( 72) covalent geometry : bond 0.00401 (23692) covalent geometry : angle 0.54776 (32228) *********************** 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 292 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6627 (tttp) REVERT: A 271 GLN cc_start: 0.7954 (mt0) cc_final: 0.7385 (tt0) REVERT: A 583 GLU cc_start: 0.7113 (mp0) cc_final: 0.6908 (mp0) REVERT: A 776 LYS cc_start: 0.8449 (tttt) cc_final: 0.8006 (ttpp) REVERT: A 990 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6994 (mp0) REVERT: A 1031 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: A 1050 MET cc_start: 0.9215 (ptp) cc_final: 0.8946 (ptm) REVERT: B 96 GLU cc_start: 0.6492 (pm20) cc_final: 0.6180 (pm20) REVERT: B 132 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6162 (mm-30) REVERT: B 231 ILE cc_start: 0.8416 (mm) cc_final: 0.7869 (pt) REVERT: B 572 THR cc_start: 0.7988 (p) cc_final: 0.7715 (t) REVERT: B 574 ASP cc_start: 0.7925 (t0) cc_final: 0.7662 (t0) REVERT: B 921 LYS cc_start: 0.8623 (mttt) cc_final: 0.7982 (ttpt) REVERT: B 1019 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7897 (ttp80) REVERT: B 1031 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: C 121 ASN cc_start: 0.6774 (m-40) cc_final: 0.5643 (t0) REVERT: C 129 LYS cc_start: 0.6602 (mtpt) cc_final: 0.6073 (mtpt) REVERT: C 140 PHE cc_start: 0.5752 (p90) cc_final: 0.5376 (p90) REVERT: C 286 THR cc_start: 0.8340 (p) cc_final: 0.8115 (p) REVERT: C 422 ASN cc_start: 0.6297 (m-40) cc_final: 0.5889 (m-40) REVERT: C 439 ASN cc_start: 0.4353 (p0) cc_final: 0.3334 (t0) REVERT: C 454 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6515 (mmt90) REVERT: C 508 TYR cc_start: 0.5711 (m-80) cc_final: 0.4595 (m-80) REVERT: C 574 ASP cc_start: 0.8323 (t0) cc_final: 0.7959 (t0) REVERT: C 772 VAL cc_start: 0.8572 (t) cc_final: 0.8200 (m) REVERT: C 983 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7647 (mtp-110) REVERT: C 1031 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8007 (mm-30) outliers start: 66 outliers final: 55 residues processed: 276 average time/residue: 0.3520 time to fit residues: 159.6476 Evaluate side-chains 272 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 240 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 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 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 393 THR Chi-restraints excluded: chain B residue 407 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 724 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 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 80 ASP 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 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 780 GLU Chi-restraints excluded: chain C residue 916 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 47 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 281 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 264 optimal weight: 0.0570 chunk 131 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 125 ASN A 641 ASN A 804 GLN A 935 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B1125 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124951 restraints weight = 27590.908| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.43 r_work: 0.3225 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23766 Z= 0.164 Angle : 0.560 9.437 32414 Z= 0.286 Chirality : 0.045 0.262 3815 Planarity : 0.004 0.059 4100 Dihedral : 6.079 65.308 3907 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.77 % Allowed : 12.46 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2859 helix: 1.81 (0.20), residues: 694 sheet: 0.13 (0.21), residues: 579 loop : -0.77 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 633 HIS 0.003 0.001 HIS A1048 PHE 0.024 0.001 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 38) link_NAG-ASN : angle 1.89709 ( 114) hydrogen bonds : bond 0.03741 ( 1009) hydrogen bonds : angle 5.40114 ( 2772) SS BOND : bond 0.00386 ( 36) SS BOND : angle 1.89799 ( 72) covalent geometry : bond 0.00393 (23692) covalent geometry : angle 0.54302 (32228) *********************** 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 283 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7289 (ttmt) cc_final: 0.6761 (tttp) REVERT: A 271 GLN cc_start: 0.7987 (mt0) cc_final: 0.7466 (tt0) REVERT: A 776 LYS cc_start: 0.8593 (tttt) cc_final: 0.8182 (ttpp) REVERT: A 990 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 1031 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: A 1050 MET cc_start: 0.9133 (ptp) cc_final: 0.8855 (ptm) REVERT: B 96 GLU cc_start: 0.6652 (pm20) cc_final: 0.6364 (pm20) REVERT: B 132 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: B 188 ASN cc_start: 0.5613 (m-40) cc_final: 0.4522 (t0) REVERT: B 231 ILE cc_start: 0.8432 (mm) cc_final: 0.7885 (pt) REVERT: B 572 THR cc_start: 0.8049 (p) cc_final: 0.7762 (t) REVERT: B 574 ASP cc_start: 0.7940 (t0) cc_final: 0.7695 (t0) REVERT: B 921 LYS cc_start: 0.8713 (mttt) cc_final: 0.8152 (ttpt) REVERT: B 1031 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: B 1125 ASN cc_start: 0.8524 (m-40) cc_final: 0.8143 (p0) REVERT: C 121 ASN cc_start: 0.6817 (m-40) cc_final: 0.5746 (t0) REVERT: C 140 PHE cc_start: 0.5833 (p90) cc_final: 0.5469 (p90) REVERT: C 286 THR cc_start: 0.8394 (p) cc_final: 0.8174 (p) REVERT: C 422 ASN cc_start: 0.6434 (m-40) cc_final: 0.6058 (m-40) REVERT: C 439 ASN cc_start: 0.4374 (p0) cc_final: 0.3391 (t0) REVERT: C 454 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6629 (mmt90) REVERT: C 508 TYR cc_start: 0.5898 (m-80) cc_final: 0.4742 (m-80) REVERT: C 555 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8164 (p) REVERT: C 574 ASP cc_start: 0.8271 (t0) cc_final: 0.7901 (t0) REVERT: C 772 VAL cc_start: 0.8668 (t) cc_final: 0.8337 (m) REVERT: C 1031 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7965 (mm-30) outliers start: 69 outliers final: 59 residues processed: 266 average time/residue: 0.3201 time to fit residues: 140.2063 Evaluate side-chains 271 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 240 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 849 LEU 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 393 THR Chi-restraints excluded: chain B residue 407 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 724 THR Chi-restraints excluded: chain B residue 791 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 1010 GLN 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 80 ASP 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 227 VAL Chi-restraints excluded: chain C residue 277 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 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS 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 916 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 116 optimal weight: 0.4980 chunk 265 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126109 restraints weight = 27633.206| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.42 r_work: 0.3251 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3608 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= 0.126 Angle : 0.546 9.599 32414 Z= 0.278 Chirality : 0.044 0.275 3815 Planarity : 0.004 0.053 4100 Dihedral : 5.946 60.055 3907 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.53 % Allowed : 12.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2859 helix: 1.96 (0.20), residues: 697 sheet: 0.18 (0.21), residues: 554 loop : -0.75 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 633 HIS 0.002 0.000 HIS A1048 PHE 0.025 0.001 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 38) link_NAG-ASN : angle 2.00767 ( 114) hydrogen bonds : bond 0.03528 ( 1009) hydrogen bonds : angle 5.30811 ( 2772) SS BOND : bond 0.00327 ( 36) SS BOND : angle 1.81825 ( 72) covalent geometry : bond 0.00295 (23692) covalent geometry : angle 0.52777 (32228) *********************** 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 283 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6640 (tttp) REVERT: A 156 GLU cc_start: 0.5164 (pp20) cc_final: 0.4554 (mm-30) REVERT: A 271 GLN cc_start: 0.7948 (mt0) cc_final: 0.7421 (tt0) REVERT: A 560 LEU cc_start: 0.8112 (mt) cc_final: 0.7879 (mt) REVERT: A 745 ASP cc_start: 0.7597 (p0) cc_final: 0.7118 (m-30) REVERT: A 776 LYS cc_start: 0.8559 (tttt) cc_final: 0.8157 (ttpp) REVERT: A 990 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7117 (mp0) REVERT: A 1031 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: A 1050 MET cc_start: 0.9087 (ptp) cc_final: 0.8825 (ptm) REVERT: B 96 GLU cc_start: 0.6688 (pm20) cc_final: 0.6392 (pm20) REVERT: B 132 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6177 (mm-30) REVERT: B 188 ASN cc_start: 0.5537 (m-40) cc_final: 0.4538 (t0) REVERT: B 572 THR cc_start: 0.8087 (p) cc_final: 0.7786 (t) REVERT: B 574 ASP cc_start: 0.7930 (t0) cc_final: 0.7682 (t0) REVERT: B 580 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: B 921 LYS cc_start: 0.8694 (mttt) cc_final: 0.8152 (ttpt) REVERT: B 1031 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8680 (mt-10) REVERT: B 1125 ASN cc_start: 0.8496 (m-40) cc_final: 0.8150 (p0) REVERT: C 121 ASN cc_start: 0.6856 (m-40) cc_final: 0.5805 (t0) REVERT: C 140 PHE cc_start: 0.5802 (p90) cc_final: 0.5437 (p90) REVERT: C 286 THR cc_start: 0.8423 (p) cc_final: 0.8207 (p) REVERT: C 422 ASN cc_start: 0.6489 (m-40) cc_final: 0.6087 (m-40) REVERT: C 439 ASN cc_start: 0.4283 (p0) cc_final: 0.3351 (t0) REVERT: C 454 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6691 (mmt90) REVERT: C 508 TYR cc_start: 0.5871 (m-80) cc_final: 0.4719 (m-80) REVERT: C 574 ASP cc_start: 0.8202 (t0) cc_final: 0.7774 (t0) REVERT: C 772 VAL cc_start: 0.8624 (t) cc_final: 0.8280 (m) REVERT: C 1031 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8061 (mp0) outliers start: 63 outliers final: 59 residues processed: 267 average time/residue: 0.3170 time to fit residues: 139.4581 Evaluate side-chains 274 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 240 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 849 LEU 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 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 407 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 580 GLN Chi-restraints excluded: chain B residue 617 CYS 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 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN 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 80 ASP 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 334 ASN Chi-restraints excluded: chain C residue 350 VAL 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 651 ILE 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 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 85 optimal weight: 0.0050 chunk 80 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 201 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 overall best weight: 0.4452 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 641 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127280 restraints weight = 27713.028| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.40 r_work: 0.3266 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23766 Z= 0.112 Angle : 0.534 9.516 32414 Z= 0.272 Chirality : 0.044 0.281 3815 Planarity : 0.004 0.052 4100 Dihedral : 5.821 56.610 3907 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 2859 helix: 2.07 (0.20), residues: 696 sheet: 0.25 (0.21), residues: 562 loop : -0.71 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 633 HIS 0.002 0.000 HIS A 954 PHE 0.026 0.001 PHE A 643 TYR 0.020 0.001 TYR A1067 ARG 0.011 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 38) link_NAG-ASN : angle 1.87847 ( 114) hydrogen bonds : bond 0.03368 ( 1009) hydrogen bonds : angle 5.20838 ( 2772) SS BOND : bond 0.00312 ( 36) SS BOND : angle 1.59378 ( 72) covalent geometry : bond 0.00259 (23692) covalent geometry : angle 0.51808 (32228) ********************** 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 276 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8117 (m-10) cc_final: 0.7833 (m-10) REVERT: A 129 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6593 (tttp) REVERT: A 156 GLU cc_start: 0.5076 (pp20) cc_final: 0.4551 (mm-30) REVERT: A 271 GLN cc_start: 0.7971 (mt0) cc_final: 0.7435 (tt0) REVERT: A 560 LEU cc_start: 0.8110 (mt) cc_final: 0.7876 (mt) REVERT: A 745 ASP cc_start: 0.7556 (p0) cc_final: 0.7000 (m-30) REVERT: A 776 LYS cc_start: 0.8535 (tttt) cc_final: 0.8147 (ttpp) REVERT: A 990 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7102 (mm-30) REVERT: A 1031 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: A 1050 MET cc_start: 0.9062 (ptp) cc_final: 0.8810 (ptm) REVERT: A 1119 ASN cc_start: 0.7663 (m-40) cc_final: 0.7260 (m-40) REVERT: B 96 GLU cc_start: 0.6674 (pm20) cc_final: 0.6372 (pm20) REVERT: B 188 ASN cc_start: 0.5472 (m-40) cc_final: 0.4529 (t0) REVERT: B 406 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6346 (mt-10) REVERT: B 572 THR cc_start: 0.8223 (p) cc_final: 0.7935 (t) REVERT: B 574 ASP cc_start: 0.7906 (t0) cc_final: 0.7695 (t0) REVERT: B 921 LYS cc_start: 0.8684 (mttt) cc_final: 0.8147 (ttpt) REVERT: B 1031 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8668 (mt-10) REVERT: B 1125 ASN cc_start: 0.8527 (m-40) cc_final: 0.8178 (p0) REVERT: C 121 ASN cc_start: 0.6796 (m-40) cc_final: 0.5826 (t0) REVERT: C 140 PHE cc_start: 0.5795 (p90) cc_final: 0.5427 (p90) REVERT: C 422 ASN cc_start: 0.6511 (m-40) cc_final: 0.6067 (m-40) REVERT: C 439 ASN cc_start: 0.4260 (p0) cc_final: 0.3337 (t0) REVERT: C 454 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6689 (mmt90) REVERT: C 508 TYR cc_start: 0.5846 (m-80) cc_final: 0.4700 (m-80) REVERT: C 555 SER cc_start: 0.8383 (t) cc_final: 0.8177 (p) REVERT: C 574 ASP cc_start: 0.8227 (t0) cc_final: 0.7805 (t0) REVERT: C 772 VAL cc_start: 0.8543 (t) cc_final: 0.8162 (m) REVERT: C 1031 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8053 (mm-30) outliers start: 57 outliers final: 47 residues processed: 260 average time/residue: 0.3146 time to fit residues: 134.6896 Evaluate side-chains 257 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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 240 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 849 LEU 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 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 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 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 41 LYS 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 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 874 THR 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 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 264 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 112 optimal weight: 0.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 804 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.178131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126158 restraints weight = 27730.160| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.40 r_work: 0.3249 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23766 Z= 0.135 Angle : 0.542 9.492 32414 Z= 0.276 Chirality : 0.044 0.280 3815 Planarity : 0.004 0.050 4100 Dihedral : 5.830 56.250 3907 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 13.55 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2859 helix: 2.05 (0.20), residues: 696 sheet: 0.12 (0.21), residues: 582 loop : -0.73 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 633 HIS 0.002 0.000 HIS A1048 PHE 0.029 0.001 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 38) link_NAG-ASN : angle 1.87245 ( 114) hydrogen bonds : bond 0.03506 ( 1009) hydrogen bonds : angle 5.22881 ( 2772) SS BOND : bond 0.00339 ( 36) SS BOND : angle 1.62198 ( 72) covalent geometry : bond 0.00319 (23692) covalent geometry : angle 0.52597 (32228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16651.56 seconds wall clock time: 290 minutes 34.29 seconds (17434.29 seconds total)