Starting phenix.real_space_refine on Sat May 24 02:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0r_42867/05_2025/8v0r_42867.cif" } resolution = 3.0 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15894 2.51 5 N 4098 2.21 5 O 4797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24903 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.94, per 1000 atoms: 0.60 Number of scatterers: 24903 At special positions: 0 Unit cell: (141.48, 129.6, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4797 8.00 N 4098 7.00 C 15894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 46 sheets defined 25.5% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.860A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.669A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.532A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.683A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.845A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.092A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.897A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.662A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.637A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.539A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.513A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.558A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.726A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.223A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.708A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.518A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.693A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.520A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.563A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.574A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) 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 984 removed outlier: 3.565A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.513A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.755A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.702A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.522A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.953A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.272A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.436A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.049A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.941A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.503A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.663A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.654A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.641A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.575A pdb=" N VAL B 130 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 120 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 128 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.943A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.249A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.413A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.641A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.858A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.611A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.533A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.534A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.283A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.984A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.768A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.065A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.040A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.528A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.377A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.571A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 966 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 7.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7943 1.35 - 1.47: 6571 1.47 - 1.60: 10808 1.60 - 1.73: 1 1.73 - 1.85: 141 Bond restraints: 25464 Sorted by residual: bond pdb=" CG PRO A 272 " pdb=" CD PRO A 272 " ideal model delta sigma weight residual 1.503 1.400 0.103 3.40e-02 8.65e+02 9.10e+00 bond pdb=" CB PRO A 272 " pdb=" CG PRO A 272 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.11e+00 bond pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.23e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.79e+00 ... (remaining 25459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 33918 2.34 - 4.68: 626 4.68 - 7.02: 75 7.02 - 9.36: 20 9.36 - 11.69: 2 Bond angle restraints: 34641 Sorted by residual: angle pdb=" CA PRO A 272 " pdb=" N PRO A 272 " pdb=" CD PRO A 272 " ideal model delta sigma weight residual 112.00 101.95 10.05 1.40e+00 5.10e-01 5.15e+01 angle pdb=" N PHE C 133 " pdb=" CA PHE C 133 " pdb=" C PHE C 133 " ideal model delta sigma weight residual 110.91 117.06 -6.15 1.17e+00 7.31e-01 2.76e+01 angle pdb=" N PRO A 272 " pdb=" CD PRO A 272 " pdb=" CG PRO A 272 " ideal model delta sigma weight residual 103.20 95.50 7.70 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C LEU B 110 " pdb=" CA LEU B 110 " pdb=" CB LEU B 110 " ideal model delta sigma weight residual 116.63 111.28 5.35 1.16e+00 7.43e-01 2.13e+01 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 ... (remaining 34636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14136 17.41 - 34.82: 1254 34.82 - 52.23: 193 52.23 - 69.64: 49 69.64 - 87.05: 37 Dihedral angle restraints: 15669 sinusoidal: 6564 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -29.54 -56.46 1 1.00e+01 1.00e-02 4.30e+01 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 -34.76 -51.24 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 139.18 -46.18 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 15666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3344 0.068 - 0.136: 637 0.136 - 0.204: 48 0.204 - 0.272: 8 0.272 - 0.340: 4 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR A 470 " pdb=" CA THR A 470 " pdb=" OG1 THR A 470 " pdb=" CG2 THR A 470 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4038 not shown) Planarity restraints: 4467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 392 " -0.018 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE A 392 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 392 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 392 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 392 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 392 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 392 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " 0.055 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 272 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO B 521 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.042 5.00e-02 4.00e+02 ... (remaining 4464 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4308 2.78 - 3.31: 20614 3.31 - 3.84: 39956 3.84 - 4.37: 45579 4.37 - 4.90: 82624 Nonbonded interactions: 193081 Sorted by model distance: nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.280 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.287 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.288 3.040 ... (remaining 193076 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 58.760 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.004 0.133 25540 Z= 0.209 Angle : 0.754 11.694 34829 Z= 0.397 Chirality : 0.053 0.340 4041 Planarity : 0.006 0.078 4434 Dihedral : 13.571 87.053 9687 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.40 (0.14), residues: 3081 helix: -0.46 (0.17), residues: 712 sheet: 0.01 (0.19), residues: 655 loop : -1.54 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 PHE 0.063 0.002 PHE A 392 TYR 0.030 0.001 TYR A 904 ARG 0.007 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 33) link_NAG-ASN : angle 2.23882 ( 99) link_BETA1-4 : bond 0.00677 ( 3) link_BETA1-4 : angle 1.86695 ( 9) hydrogen bonds : bond 0.20367 ( 966) hydrogen bonds : angle 7.52625 ( 2685) SS BOND : bond 0.00553 ( 40) SS BOND : angle 1.53008 ( 80) covalent geometry : bond 0.00449 (25464) covalent geometry : angle 0.74221 (34641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.649 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8228 (mt) cc_final: 0.8004 (mt) REVERT: A 869 MET cc_start: 0.8838 (mtt) cc_final: 0.8553 (mtt) REVERT: B 641 ASN cc_start: 0.6829 (m110) cc_final: 0.6496 (m110) REVERT: B 697 MET cc_start: 0.8903 (ptm) cc_final: 0.8698 (ptm) REVERT: B 731 MET cc_start: 0.9010 (ptt) cc_final: 0.8620 (ptt) REVERT: C 558 LYS cc_start: 0.8207 (mptt) cc_final: 0.7991 (mmtp) REVERT: C 574 ASP cc_start: 0.7537 (t70) cc_final: 0.7101 (t0) outliers start: 0 outliers final: 2 residues processed: 271 average time/residue: 1.2186 time to fit residues: 389.4264 Evaluate side-chains 193 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain C residue 198 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.7980 chunk 236 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 0.0570 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 405 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B 317 ASN B 417 ASN B 935 GLN B1088 HIS C 334 ASN C 901 GLN C1005 GLN C1088 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131923 restraints weight = 29092.434| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.56 r_work: 0.3297 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25540 Z= 0.108 Angle : 0.517 6.127 34829 Z= 0.272 Chirality : 0.044 0.267 4041 Planarity : 0.004 0.061 4434 Dihedral : 6.258 54.729 4102 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 0.85 % Allowed : 6.34 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3081 helix: 1.20 (0.19), residues: 727 sheet: 0.23 (0.19), residues: 697 loop : -1.41 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 PHE 0.022 0.001 PHE A 168 TYR 0.011 0.001 TYR B 837 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 33) link_NAG-ASN : angle 1.64008 ( 99) link_BETA1-4 : bond 0.00416 ( 3) link_BETA1-4 : angle 1.11388 ( 9) hydrogen bonds : bond 0.04656 ( 966) hydrogen bonds : angle 5.26681 ( 2685) SS BOND : bond 0.00353 ( 40) SS BOND : angle 1.08555 ( 80) covalent geometry : bond 0.00236 (25464) covalent geometry : angle 0.50775 (34641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 3.071 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7038 (t) REVERT: A 869 MET cc_start: 0.8953 (mtt) cc_final: 0.8687 (mtt) REVERT: A 1050 MET cc_start: 0.8730 (ptm) cc_final: 0.8517 (ptt) REVERT: B 641 ASN cc_start: 0.6944 (m110) cc_final: 0.6620 (m110) REVERT: B 731 MET cc_start: 0.9167 (ptt) cc_final: 0.8776 (ptt) outliers start: 23 outliers final: 10 residues processed: 242 average time/residue: 1.0236 time to fit residues: 298.8657 Evaluate side-chains 212 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 142 optimal weight: 0.0030 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 265 optimal weight: 0.2980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN A 405 ASN A 519 HIS B 188 ASN B 207 HIS B 613 GLN B 675 GLN B 762 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129096 restraints weight = 29097.458| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.62 r_work: 0.3201 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25540 Z= 0.103 Angle : 0.491 8.608 34829 Z= 0.257 Chirality : 0.044 0.256 4041 Planarity : 0.004 0.057 4434 Dihedral : 5.612 53.384 4098 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 1.22 % Allowed : 8.40 % Favored : 90.39 % 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: -0.26 (0.15), residues: 3081 helix: 1.76 (0.20), residues: 722 sheet: 0.30 (0.19), residues: 705 loop : -1.32 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.016 0.001 HIS C 207 PHE 0.028 0.001 PHE A 168 TYR 0.012 0.001 TYR C 837 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 33) link_NAG-ASN : angle 1.60190 ( 99) link_BETA1-4 : bond 0.00405 ( 3) link_BETA1-4 : angle 1.09927 ( 9) hydrogen bonds : bond 0.04337 ( 966) hydrogen bonds : angle 4.84828 ( 2685) SS BOND : bond 0.00292 ( 40) SS BOND : angle 1.06306 ( 80) covalent geometry : bond 0.00230 (25464) covalent geometry : angle 0.48224 (34641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: B 354 ASN cc_start: 0.8069 (m110) cc_final: 0.7704 (t0) REVERT: B 641 ASN cc_start: 0.6878 (m110) cc_final: 0.6543 (m110) REVERT: B 731 MET cc_start: 0.9242 (ptt) cc_final: 0.8807 (ptt) REVERT: C 574 ASP cc_start: 0.8230 (t70) cc_final: 0.7870 (t0) REVERT: C 994 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7354 (t70) REVERT: C 1002 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7625 (mp-120) outliers start: 33 outliers final: 18 residues processed: 229 average time/residue: 0.9627 time to fit residues: 267.6252 Evaluate side-chains 217 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 44 optimal weight: 0.3980 chunk 40 optimal weight: 0.0060 chunk 22 optimal weight: 0.0070 chunk 200 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 0.0020 chunk 231 optimal weight: 4.9990 overall best weight: 0.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 188 ASN B 207 HIS B1002 GLN C 339 HIS C 613 GLN C 762 GLN C 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131869 restraints weight = 29554.076| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.67 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25540 Z= 0.086 Angle : 0.462 7.410 34829 Z= 0.241 Chirality : 0.043 0.272 4041 Planarity : 0.003 0.056 4434 Dihedral : 5.161 53.577 4098 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 0.99 % Allowed : 9.58 % Favored : 89.43 % 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: -0.03 (0.15), residues: 3081 helix: 2.06 (0.20), residues: 727 sheet: 0.37 (0.19), residues: 707 loop : -1.20 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.029 0.001 PHE A 168 TYR 0.011 0.001 TYR A1067 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 33) link_NAG-ASN : angle 1.51838 ( 99) link_BETA1-4 : bond 0.00419 ( 3) link_BETA1-4 : angle 1.01253 ( 9) hydrogen bonds : bond 0.03756 ( 966) hydrogen bonds : angle 4.61565 ( 2685) SS BOND : bond 0.00308 ( 40) SS BOND : angle 0.94103 ( 80) covalent geometry : bond 0.00180 (25464) covalent geometry : angle 0.45371 (34641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 2.586 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6973 (t) REVERT: B 177 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5635 (pp-130) REVERT: B 354 ASN cc_start: 0.8024 (m110) cc_final: 0.7703 (t0) REVERT: B 641 ASN cc_start: 0.6899 (m110) cc_final: 0.6549 (m110) REVERT: B 731 MET cc_start: 0.9248 (ptt) cc_final: 0.8981 (ptt) REVERT: C 574 ASP cc_start: 0.8168 (t70) cc_final: 0.7813 (t0) REVERT: C 994 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7263 (t70) REVERT: C 1002 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7983 (mm-40) outliers start: 27 outliers final: 14 residues processed: 236 average time/residue: 0.9806 time to fit residues: 281.5590 Evaluate side-chains 222 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 79 optimal weight: 2.9990 chunk 276 optimal weight: 0.0070 chunk 201 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 225 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 188 ASN B 207 HIS B 448 ASN B 762 GLN C 339 HIS C 394 ASN C 613 GLN C 762 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122510 restraints weight = 29567.410| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.79 r_work: 0.3090 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25540 Z= 0.247 Angle : 0.641 8.556 34829 Z= 0.332 Chirality : 0.049 0.325 4041 Planarity : 0.004 0.054 4434 Dihedral : 5.812 55.480 4098 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 2.14 % Allowed : 10.17 % Favored : 87.70 % 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: -0.40 (0.15), residues: 3081 helix: 1.59 (0.20), residues: 736 sheet: 0.12 (0.19), residues: 673 loop : -1.33 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.008 0.002 HIS C1048 PHE 0.035 0.002 PHE A 906 TYR 0.015 0.002 TYR B 37 ARG 0.006 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 33) link_NAG-ASN : angle 2.08456 ( 99) link_BETA1-4 : bond 0.00427 ( 3) link_BETA1-4 : angle 1.73481 ( 9) hydrogen bonds : bond 0.06264 ( 966) hydrogen bonds : angle 4.95798 ( 2685) SS BOND : bond 0.00527 ( 40) SS BOND : angle 1.93762 ( 80) covalent geometry : bond 0.00621 (25464) covalent geometry : angle 0.62598 (34641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7072 (t) REVERT: A 335 LEU cc_start: 0.8929 (mm) cc_final: 0.8686 (mt) REVERT: A 564 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: A 675 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7534 (mm110) REVERT: A 1118 ASP cc_start: 0.8058 (m-30) cc_final: 0.7846 (m-30) REVERT: B 52 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7666 (tp40) REVERT: B 354 ASN cc_start: 0.8074 (m110) cc_final: 0.7684 (t0) REVERT: B 458 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7565 (mtpt) REVERT: B 731 MET cc_start: 0.9333 (ptt) cc_final: 0.8877 (ptt) REVERT: B 934 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 1138 TYR cc_start: 0.7775 (t80) cc_final: 0.7517 (t80) REVERT: C 319 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7628 (ttm110) REVERT: C 383 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8703 (m) REVERT: C 574 ASP cc_start: 0.8140 (t70) cc_final: 0.7843 (t0) REVERT: C 776 LYS cc_start: 0.8778 (tttp) cc_final: 0.8484 (tttm) REVERT: C 981 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 58 outliers final: 27 residues processed: 245 average time/residue: 1.0889 time to fit residues: 318.2579 Evaluate side-chains 225 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 266 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B1002 GLN C 339 HIS C 613 GLN C 762 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126265 restraints weight = 29271.179| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.77 r_work: 0.3164 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25540 Z= 0.103 Angle : 0.500 5.350 34829 Z= 0.260 Chirality : 0.044 0.299 4041 Planarity : 0.003 0.056 4434 Dihedral : 5.323 54.893 4098 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.77 % Allowed : 11.64 % Favored : 86.59 % 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: -0.12 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 745 sheet: 0.25 (0.19), residues: 711 loop : -1.21 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS C 339 PHE 0.026 0.001 PHE A 168 TYR 0.013 0.001 TYR C1067 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 33) link_NAG-ASN : angle 1.73375 ( 99) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 1.26267 ( 9) hydrogen bonds : bond 0.04426 ( 966) hydrogen bonds : angle 4.61915 ( 2685) SS BOND : bond 0.00369 ( 40) SS BOND : angle 1.35132 ( 80) covalent geometry : bond 0.00227 (25464) covalent geometry : angle 0.48777 (34641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 2.604 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6170 (mtp180) cc_final: 0.5798 (mmm-85) REVERT: A 166 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6991 (t) REVERT: A 675 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7473 (mm110) REVERT: B 52 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 354 ASN cc_start: 0.7942 (m110) cc_final: 0.7645 (t0) REVERT: B 731 MET cc_start: 0.9352 (ptt) cc_final: 0.8992 (ptt) REVERT: B 1092 GLU cc_start: 0.8187 (pm20) cc_final: 0.7656 (pt0) REVERT: B 1138 TYR cc_start: 0.7717 (t80) cc_final: 0.7475 (t80) REVERT: C 574 ASP cc_start: 0.8090 (t70) cc_final: 0.7797 (t0) REVERT: C 935 GLN cc_start: 0.7503 (tt0) cc_final: 0.7271 (tt0) REVERT: C 981 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 48 outliers final: 27 residues processed: 230 average time/residue: 0.9509 time to fit residues: 266.5918 Evaluate side-chains 213 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 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 207 HIS A 405 ASN B 188 ASN B 207 HIS B 448 ASN B1101 HIS C 339 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123666 restraints weight = 29417.800| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.75 r_work: 0.3084 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25540 Z= 0.176 Angle : 0.555 6.456 34829 Z= 0.288 Chirality : 0.046 0.318 4041 Planarity : 0.004 0.057 4434 Dihedral : 5.422 54.312 4098 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 1.84 % Allowed : 12.67 % Favored : 85.49 % 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: -0.18 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 733 sheet: 0.27 (0.19), residues: 682 loop : -1.26 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 PHE 0.026 0.002 PHE A 168 TYR 0.013 0.001 TYR C 837 ARG 0.009 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 33) link_NAG-ASN : angle 1.86947 ( 99) link_BETA1-4 : bond 0.00489 ( 3) link_BETA1-4 : angle 1.49478 ( 9) hydrogen bonds : bond 0.05161 ( 966) hydrogen bonds : angle 4.67164 ( 2685) SS BOND : bond 0.00446 ( 40) SS BOND : angle 1.71054 ( 80) covalent geometry : bond 0.00436 (25464) covalent geometry : angle 0.54122 (34641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 2.625 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6084 (mtp180) cc_final: 0.5711 (mmm-85) REVERT: A 166 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7065 (t) REVERT: A 675 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7359 (mm110) REVERT: B 52 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7569 (tp40) REVERT: B 319 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6983 (mtt180) REVERT: B 354 ASN cc_start: 0.7963 (m110) cc_final: 0.7637 (t0) REVERT: B 458 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7609 (mtpt) REVERT: B 731 MET cc_start: 0.9355 (ptt) cc_final: 0.8993 (ptt) REVERT: B 934 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (mp) REVERT: B 1092 GLU cc_start: 0.8176 (pm20) cc_final: 0.7644 (pt0) REVERT: B 1138 TYR cc_start: 0.7773 (t80) cc_final: 0.7478 (t80) REVERT: C 319 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7572 (ttm110) REVERT: C 459 SER cc_start: 0.8711 (p) cc_final: 0.8405 (t) REVERT: C 981 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8418 (mt) outliers start: 50 outliers final: 29 residues processed: 225 average time/residue: 0.9370 time to fit residues: 257.3468 Evaluate side-chains 218 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS B 188 ASN B 207 HIS B 448 ASN C 207 HIS C 339 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124126 restraints weight = 29422.895| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.67 r_work: 0.3113 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25540 Z= 0.150 Angle : 0.539 11.123 34829 Z= 0.279 Chirality : 0.045 0.300 4041 Planarity : 0.004 0.056 4434 Dihedral : 5.399 53.971 4098 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 1.95 % Allowed : 13.26 % Favored : 84.79 % 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: 3081 helix: 1.85 (0.20), residues: 739 sheet: 0.19 (0.19), residues: 710 loop : -1.19 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.011 0.001 HIS C 207 PHE 0.026 0.001 PHE A 168 TYR 0.014 0.001 TYR C1067 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 33) link_NAG-ASN : angle 1.83712 ( 99) link_BETA1-4 : bond 0.00446 ( 3) link_BETA1-4 : angle 1.44806 ( 9) hydrogen bonds : bond 0.04912 ( 966) hydrogen bonds : angle 4.62353 ( 2685) SS BOND : bond 0.00424 ( 40) SS BOND : angle 1.58910 ( 80) covalent geometry : bond 0.00366 (25464) covalent geometry : angle 0.52564 (34641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5895 (mtp180) cc_final: 0.5597 (mmm-85) REVERT: A 166 CYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6874 (t) REVERT: A 675 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7377 (mm110) REVERT: B 52 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 354 ASN cc_start: 0.7980 (m110) cc_final: 0.7670 (t0) REVERT: B 458 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7615 (mtpt) REVERT: B 731 MET cc_start: 0.9356 (ptt) cc_final: 0.8981 (ptt) REVERT: B 934 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 1092 GLU cc_start: 0.8270 (pm20) cc_final: 0.7712 (pt0) REVERT: B 1138 TYR cc_start: 0.7834 (t80) cc_final: 0.7574 (t80) REVERT: C 319 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7569 (ttm110) REVERT: C 459 SER cc_start: 0.8715 (p) cc_final: 0.8487 (t) REVERT: C 935 GLN cc_start: 0.7496 (tt0) cc_final: 0.7250 (tt0) REVERT: C 981 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8455 (mt) REVERT: C 994 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7556 (t70) outliers start: 53 outliers final: 36 residues processed: 233 average time/residue: 0.9958 time to fit residues: 283.3001 Evaluate side-chains 231 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 188 ASN B 207 HIS B 394 ASN B 448 ASN B1005 GLN C 339 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124601 restraints weight = 29393.863| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.67 r_work: 0.3116 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25540 Z= 0.132 Angle : 0.525 9.658 34829 Z= 0.273 Chirality : 0.045 0.315 4041 Planarity : 0.004 0.056 4434 Dihedral : 5.298 53.910 4098 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 1.80 % Allowed : 13.48 % Favored : 84.71 % 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: -0.07 (0.15), residues: 3081 helix: 1.94 (0.20), residues: 739 sheet: 0.27 (0.19), residues: 696 loop : -1.17 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.024 0.001 PHE A 168 TYR 0.016 0.001 TYR A 421 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 33) link_NAG-ASN : angle 1.78758 ( 99) link_BETA1-4 : bond 0.00509 ( 3) link_BETA1-4 : angle 1.40481 ( 9) hydrogen bonds : bond 0.04655 ( 966) hydrogen bonds : angle 4.57247 ( 2685) SS BOND : bond 0.00414 ( 40) SS BOND : angle 1.48818 ( 80) covalent geometry : bond 0.00316 (25464) covalent geometry : angle 0.51180 (34641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 2.818 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5862 (mtp180) cc_final: 0.5576 (mmm-85) REVERT: A 166 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6873 (t) REVERT: A 675 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7384 (mm110) REVERT: B 52 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 354 ASN cc_start: 0.7970 (m110) cc_final: 0.7681 (t0) REVERT: B 458 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7613 (mtpt) REVERT: B 731 MET cc_start: 0.9362 (ptt) cc_final: 0.8993 (ptt) REVERT: B 1092 GLU cc_start: 0.8276 (pm20) cc_final: 0.7723 (pt0) REVERT: B 1138 TYR cc_start: 0.7819 (t80) cc_final: 0.7602 (t80) REVERT: C 319 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7570 (ttm110) REVERT: C 459 SER cc_start: 0.8728 (p) cc_final: 0.8502 (t) REVERT: C 935 GLN cc_start: 0.7429 (tt0) cc_final: 0.7189 (tt0) REVERT: C 981 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8456 (mt) REVERT: C 994 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7551 (t70) outliers start: 49 outliers final: 33 residues processed: 225 average time/residue: 1.0261 time to fit residues: 279.1372 Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 302 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 188 ASN B 207 HIS B1005 GLN C 339 HIS C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124825 restraints weight = 29344.063| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.66 r_work: 0.3130 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25540 Z= 0.120 Angle : 0.516 9.848 34829 Z= 0.268 Chirality : 0.044 0.323 4041 Planarity : 0.003 0.056 4434 Dihedral : 5.246 53.923 4098 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 1.33 % Allowed : 14.03 % Favored : 84.64 % 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: -0.02 (0.15), residues: 3081 helix: 1.97 (0.20), residues: 745 sheet: 0.29 (0.19), residues: 695 loop : -1.13 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.025 0.001 PHE A 168 TYR 0.013 0.001 TYR C1067 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 33) link_NAG-ASN : angle 1.76701 ( 99) link_BETA1-4 : bond 0.00489 ( 3) link_BETA1-4 : angle 1.36626 ( 9) hydrogen bonds : bond 0.04499 ( 966) hydrogen bonds : angle 4.53820 ( 2685) SS BOND : bond 0.00399 ( 40) SS BOND : angle 1.46102 ( 80) covalent geometry : bond 0.00280 (25464) covalent geometry : angle 0.50345 (34641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 5.899 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5896 (mtp180) cc_final: 0.5627 (mmm-85) REVERT: A 166 CYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6834 (t) REVERT: A 675 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7367 (mm110) REVERT: A 869 MET cc_start: 0.9059 (mtt) cc_final: 0.8787 (mtt) REVERT: B 52 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 354 ASN cc_start: 0.7921 (m110) cc_final: 0.7631 (t0) REVERT: B 458 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7585 (mtpt) REVERT: B 731 MET cc_start: 0.9358 (ptt) cc_final: 0.8986 (ptt) REVERT: B 1092 GLU cc_start: 0.8257 (pm20) cc_final: 0.7698 (pt0) REVERT: B 1138 TYR cc_start: 0.7800 (t80) cc_final: 0.7591 (t80) REVERT: C 319 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7587 (ttm110) REVERT: C 375 PHE cc_start: 0.7804 (m-10) cc_final: 0.7491 (t80) REVERT: C 459 SER cc_start: 0.8743 (p) cc_final: 0.8518 (t) REVERT: C 935 GLN cc_start: 0.7413 (tt0) cc_final: 0.7189 (tt0) REVERT: C 981 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 994 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7496 (t70) outliers start: 36 outliers final: 33 residues processed: 220 average time/residue: 1.0873 time to fit residues: 294.5750 Evaluate side-chains 227 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 281 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.0070 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 188 ASN B 207 HIS B1005 GLN C 339 HIS C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123816 restraints weight = 29461.291| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.71 r_work: 0.3108 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25540 Z= 0.149 Angle : 0.542 10.253 34829 Z= 0.281 Chirality : 0.045 0.326 4041 Planarity : 0.004 0.055 4434 Dihedral : 5.314 54.174 4098 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 1.73 % Allowed : 13.70 % Favored : 84.57 % 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: -0.09 (0.15), residues: 3081 helix: 1.91 (0.20), residues: 739 sheet: 0.26 (0.19), residues: 698 loop : -1.17 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.025 0.001 PHE A 168 TYR 0.017 0.001 TYR A 421 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 33) link_NAG-ASN : angle 1.82279 ( 99) link_BETA1-4 : bond 0.00511 ( 3) link_BETA1-4 : angle 1.47505 ( 9) hydrogen bonds : bond 0.04861 ( 966) hydrogen bonds : angle 4.58073 ( 2685) SS BOND : bond 0.00423 ( 40) SS BOND : angle 1.61733 ( 80) covalent geometry : bond 0.00362 (25464) covalent geometry : angle 0.52808 (34641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12778.22 seconds wall clock time: 221 minutes 37.71 seconds (13297.71 seconds total)