Starting phenix.real_space_refine on Mon Aug 25 03:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0r_42867/08_2025/8v0r_42867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0r_42867/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v0r_42867/08_2025/8v0r_42867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0r_42867/08_2025/8v0r_42867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v0r_42867/08_2025/8v0r_42867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0r_42867/08_2025/8v0r_42867.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.99, per 1000 atoms: 0.20 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: 1.86 Conformation dependent library (CDL) restraints added in 866.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.78 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: 4.93 Time building geometry restraints manager: 2.40 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: 0.02 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.790 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 498 TYR 0.030 0.001 TYR A 904 PHE 0.063 0.002 PHE A 392 TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00449 (25464) covalent geometry : angle 0.74221 (34641) SS BOND : bond 0.00553 ( 40) SS BOND : angle 1.53008 ( 80) hydrogen bonds : bond 0.20367 ( 966) hydrogen bonds : angle 7.52625 ( 2685) link_BETA1-4 : bond 0.00677 ( 3) link_BETA1-4 : angle 1.86695 ( 9) link_NAG-ASN : bond 0.00381 ( 33) link_NAG-ASN : angle 2.23882 ( 99) *********************** 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 : 0.601 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: 0.8552 (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: 0.8697 (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: 0.5338 time to fit residues: 169.0391 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 : 0.740 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B 317 ASN B 417 ASN B 613 GLN B 935 GLN B1088 HIS C 334 ASN C 901 GLN C1005 GLN C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129869 restraints weight = 29271.486| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.63 r_work: 0.3279 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25540 Z= 0.126 Angle : 0.534 6.100 34829 Z= 0.280 Chirality : 0.045 0.280 4041 Planarity : 0.004 0.060 4434 Dihedral : 6.330 55.126 4102 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 0.96 % Allowed : 6.37 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3081 helix: 1.20 (0.19), residues: 721 sheet: 0.16 (0.19), residues: 687 loop : -1.41 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.012 0.001 TYR B 837 PHE 0.021 0.001 PHE A 168 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (25464) covalent geometry : angle 0.52420 (34641) SS BOND : bond 0.00352 ( 40) SS BOND : angle 1.21345 ( 80) hydrogen bonds : bond 0.04850 ( 966) hydrogen bonds : angle 5.24878 ( 2685) link_BETA1-4 : bond 0.00457 ( 3) link_BETA1-4 : angle 1.11770 ( 9) link_NAG-ASN : bond 0.00344 ( 33) link_NAG-ASN : angle 1.66247 ( 99) *********************** 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 253 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7074 (t) REVERT: A 869 MET cc_start: 0.9068 (mtt) cc_final: 0.8824 (mtt) REVERT: A 1050 MET cc_start: 0.8930 (ptm) cc_final: 0.8677 (ptt) REVERT: B 177 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.5797 (pp-130) REVERT: B 641 ASN cc_start: 0.7090 (m110) cc_final: 0.6756 (m110) REVERT: B 731 MET cc_start: 0.9249 (ptt) cc_final: 0.8844 (ptt) REVERT: C 574 ASP cc_start: 0.8331 (t70) cc_final: 0.8130 (OUTLIER) outliers start: 26 outliers final: 13 residues processed: 234 average time/residue: 0.4655 time to fit residues: 130.7865 Evaluate side-chains 215 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 A residue 1136 THR Chi-restraints excluded: chain B residue 176 LEU 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 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 828 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 41 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.0000 chunk 195 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- 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 B 188 ASN B 207 HIS B 354 ASN B 448 ASN B 675 GLN C 66 HIS C 207 HIS C 394 ASN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123444 restraints weight = 29500.769| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.79 r_work: 0.3071 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25540 Z= 0.218 Angle : 0.623 13.876 34829 Z= 0.323 Chirality : 0.049 0.324 4041 Planarity : 0.004 0.056 4434 Dihedral : 6.145 55.881 4098 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 8.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3081 helix: 1.33 (0.20), residues: 732 sheet: 0.03 (0.19), residues: 682 loop : -1.44 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 24 TYR 0.014 0.002 TYR C 837 PHE 0.032 0.002 PHE A 906 TRP 0.011 0.002 TRP A 436 HIS 0.017 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00539 (25464) covalent geometry : angle 0.60902 (34641) SS BOND : bond 0.00476 ( 40) SS BOND : angle 1.75220 ( 80) hydrogen bonds : bond 0.06096 ( 966) hydrogen bonds : angle 5.03429 ( 2685) link_BETA1-4 : bond 0.00408 ( 3) link_BETA1-4 : angle 1.62377 ( 9) link_NAG-ASN : bond 0.00321 ( 33) link_NAG-ASN : angle 2.03771 ( 99) *********************** 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 273 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7127 (t) REVERT: A 564 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: A 869 MET cc_start: 0.9117 (mtt) cc_final: 0.8839 (mtt) REVERT: B 52 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7718 (tp40) REVERT: B 177 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5638 (pp-130) REVERT: B 731 MET cc_start: 0.9328 (ptt) cc_final: 0.8807 (ptt) REVERT: B 814 LYS cc_start: 0.7135 (mptt) cc_final: 0.6740 (mppt) REVERT: B 1138 TYR cc_start: 0.7809 (t80) cc_final: 0.7525 (t80) REVERT: C 319 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7544 (ttm110) REVERT: C 383 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8636 (m) REVERT: C 574 ASP cc_start: 0.8163 (t70) cc_final: 0.7880 (t0) REVERT: C 776 LYS cc_start: 0.8845 (tttp) cc_final: 0.8543 (tttm) REVERT: C 981 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (mt) outliers start: 53 outliers final: 24 residues processed: 252 average time/residue: 0.4874 time to fit residues: 145.9156 Evaluate side-chains 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 177 MET 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 441 LEU Chi-restraints excluded: chain B residue 468 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 900 MET Chi-restraints excluded: chain C residue 335 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 271 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 273 optimal weight: 0.3980 chunk 225 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** A 901 GLN B 188 ASN B 207 HIS B 675 GLN C 314 GLN C 339 HIS C 613 GLN C 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124922 restraints weight = 29257.863| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.69 r_work: 0.3151 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25540 Z= 0.110 Angle : 0.512 8.215 34829 Z= 0.267 Chirality : 0.044 0.284 4041 Planarity : 0.003 0.058 4434 Dihedral : 5.607 54.403 4098 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 1.07 % Allowed : 11.20 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3081 helix: 1.72 (0.20), residues: 744 sheet: 0.20 (0.19), residues: 709 loop : -1.31 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.011 0.001 TYR A1067 PHE 0.029 0.001 PHE A 168 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00252 (25464) covalent geometry : angle 0.50001 (34641) SS BOND : bond 0.00393 ( 40) SS BOND : angle 1.39314 ( 80) hydrogen bonds : bond 0.04521 ( 966) hydrogen bonds : angle 4.72375 ( 2685) link_BETA1-4 : bond 0.00480 ( 3) link_BETA1-4 : angle 1.23862 ( 9) link_NAG-ASN : bond 0.00317 ( 33) link_NAG-ASN : angle 1.74637 ( 99) *********************** 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 239 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6060 (mtp180) cc_final: 0.5650 (mmm-85) REVERT: A 166 CYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7061 (t) REVERT: A 869 MET cc_start: 0.9043 (mtt) cc_final: 0.8792 (mtt) REVERT: B 239 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8241 (mm110) REVERT: B 554 GLU cc_start: 0.7535 (mp0) cc_final: 0.7182 (mp0) REVERT: B 731 MET cc_start: 0.9335 (ptt) cc_final: 0.8969 (ptt) REVERT: B 814 LYS cc_start: 0.7036 (mptt) cc_final: 0.6615 (mtmt) REVERT: B 1138 TYR cc_start: 0.7718 (t80) cc_final: 0.7459 (t80) outliers start: 29 outliers final: 21 residues processed: 226 average time/residue: 0.4638 time to fit residues: 124.6254 Evaluate side-chains 211 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain A residue 350 VAL 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 B residue 197 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 532 ASN 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 C residue 210 ILE Chi-restraints excluded: chain C residue 350 VAL 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 859 THR Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 41 optimal weight: 0.6980 chunk 244 optimal weight: 0.0020 chunk 273 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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** B 99 ASN B 188 ASN B 207 HIS B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.167304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128027 restraints weight = 29459.336| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.66 r_work: 0.3170 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25540 Z= 0.093 Angle : 0.479 6.910 34829 Z= 0.249 Chirality : 0.043 0.292 4041 Planarity : 0.003 0.058 4434 Dihedral : 5.191 53.976 4098 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 1.69 % Allowed : 11.93 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.15), residues: 3081 helix: 2.04 (0.20), residues: 737 sheet: 0.30 (0.19), residues: 708 loop : -1.18 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.014 0.001 TYR A 421 PHE 0.027 0.001 PHE A 168 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00204 (25464) covalent geometry : angle 0.46824 (34641) SS BOND : bond 0.00463 ( 40) SS BOND : angle 1.19499 ( 80) hydrogen bonds : bond 0.03979 ( 966) hydrogen bonds : angle 4.52247 ( 2685) link_BETA1-4 : bond 0.00495 ( 3) link_BETA1-4 : angle 1.14365 ( 9) link_NAG-ASN : bond 0.00302 ( 33) link_NAG-ASN : angle 1.62373 ( 99) *********************** 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 257 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6029 (mtp180) cc_final: 0.5650 (mmm-85) REVERT: A 166 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6969 (t) REVERT: B 354 ASN cc_start: 0.7929 (m-40) cc_final: 0.7637 (t0) REVERT: B 731 MET cc_start: 0.9339 (ptt) cc_final: 0.8992 (ptt) REVERT: C 494 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (m) REVERT: C 558 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8249 (mmtm) REVERT: C 574 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7787 (t0) REVERT: C 981 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (mt) REVERT: C 994 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7415 (t70) outliers start: 46 outliers final: 25 residues processed: 241 average time/residue: 0.4647 time to fit residues: 135.1102 Evaluate side-chains 221 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 859 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 518 LEU 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 C residue 210 ILE 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 574 ASP 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 Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 14 optimal weight: 0.0270 chunk 257 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 277 optimal weight: 0.3980 chunk 263 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 675 GLN C 339 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126467 restraints weight = 29441.232| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.64 r_work: 0.3179 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25540 Z= 0.099 Angle : 0.480 5.928 34829 Z= 0.250 Chirality : 0.043 0.300 4041 Planarity : 0.003 0.055 4434 Dihedral : 5.063 53.707 4098 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 1.58 % Allowed : 12.82 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3081 helix: 2.07 (0.20), residues: 745 sheet: 0.35 (0.19), residues: 712 loop : -1.12 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.012 0.001 TYR C1067 PHE 0.026 0.001 PHE A 168 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00223 (25464) covalent geometry : angle 0.47024 (34641) SS BOND : bond 0.00339 ( 40) SS BOND : angle 1.14875 ( 80) hydrogen bonds : bond 0.04003 ( 966) hydrogen bonds : angle 4.43952 ( 2685) link_BETA1-4 : bond 0.00494 ( 3) link_BETA1-4 : angle 1.17541 ( 9) link_NAG-ASN : bond 0.00291 ( 33) link_NAG-ASN : angle 1.61450 ( 99) *********************** 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 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6088 (mtp180) cc_final: 0.5718 (mmm-85) REVERT: A 166 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6991 (t) REVERT: B 354 ASN cc_start: 0.7897 (m-40) cc_final: 0.7616 (t0) REVERT: B 731 MET cc_start: 0.9347 (ptt) cc_final: 0.9006 (ptt) REVERT: B 1092 GLU cc_start: 0.8207 (pm20) cc_final: 0.7669 (pt0) REVERT: B 1138 TYR cc_start: 0.7744 (t80) cc_final: 0.7480 (t80) REVERT: C 390 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7239 (pt) REVERT: C 494 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8738 (m) REVERT: C 574 ASP cc_start: 0.8161 (t70) cc_final: 0.7860 (t0) REVERT: C 828 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7438 (mm) REVERT: C 981 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8391 (mt) REVERT: C 994 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (t70) outliers start: 43 outliers final: 27 residues processed: 227 average time/residue: 0.4271 time to fit residues: 116.9372 Evaluate side-chains 218 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 576 VAL 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 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 532 ASN 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 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 383 SER Chi-restraints excluded: chain C residue 390 LEU 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 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 Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 57 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 130 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 394 ASN C 493 GLN C 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122845 restraints weight = 29265.399| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.65 r_work: 0.3104 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1961 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= 0.169 Angle : 0.555 7.267 34829 Z= 0.287 Chirality : 0.046 0.311 4041 Planarity : 0.004 0.055 4434 Dihedral : 5.370 54.608 4098 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 12.85 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3081 helix: 1.90 (0.20), residues: 745 sheet: 0.34 (0.19), residues: 691 loop : -1.19 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.013 0.001 TYR C1067 PHE 0.024 0.002 PHE A 168 TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (25464) covalent geometry : angle 0.54074 (34641) SS BOND : bond 0.00422 ( 40) SS BOND : angle 1.67636 ( 80) hydrogen bonds : bond 0.05166 ( 966) hydrogen bonds : angle 4.63763 ( 2685) link_BETA1-4 : bond 0.00464 ( 3) link_BETA1-4 : angle 1.50054 ( 9) link_NAG-ASN : bond 0.00283 ( 33) link_NAG-ASN : angle 1.85305 ( 99) *********************** 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 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5741 (mmm-85) REVERT: A 166 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7041 (t) REVERT: B 52 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: B 731 MET cc_start: 0.9402 (ptt) cc_final: 0.9022 (ptt) REVERT: B 1092 GLU cc_start: 0.8232 (pm20) cc_final: 0.7704 (pt0) REVERT: B 1138 TYR cc_start: 0.7811 (t80) cc_final: 0.7534 (t80) REVERT: C 271 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: C 319 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7624 (ttm110) REVERT: C 383 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8633 (m) REVERT: C 390 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7339 (pt) REVERT: C 459 SER cc_start: 0.8728 (p) cc_final: 0.8512 (t) REVERT: C 494 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8692 (m) REVERT: C 574 ASP cc_start: 0.8215 (t70) cc_final: 0.7885 (t0) REVERT: C 981 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 994 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7566 (t70) outliers start: 60 outliers final: 31 residues processed: 247 average time/residue: 0.4391 time to fit residues: 129.7276 Evaluate side-chains 232 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 576 VAL 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 468 ILE Chi-restraints excluded: chain B residue 532 ASN 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 C residue 210 ILE Chi-restraints excluded: chain C residue 271 GLN 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 390 LEU 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 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 Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 177 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 0.3980 chunk 166 optimal weight: 0.7980 chunk 207 optimal weight: 0.0470 chunk 146 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 121 optimal weight: 0.2980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN A 675 GLN B 188 ASN B 207 HIS B1005 GLN C 394 ASN C 417 ASN C 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.167601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128367 restraints weight = 29445.814| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.66 r_work: 0.3196 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25540 Z= 0.090 Angle : 0.474 5.489 34829 Z= 0.247 Chirality : 0.043 0.269 4041 Planarity : 0.003 0.056 4434 Dihedral : 4.987 54.870 4098 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 1.25 % Allowed : 14.07 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3081 helix: 2.17 (0.20), residues: 746 sheet: 0.41 (0.19), residues: 708 loop : -1.03 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 646 TYR 0.013 0.001 TYR C1067 PHE 0.025 0.001 PHE A 168 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00192 (25464) covalent geometry : angle 0.46366 (34641) SS BOND : bond 0.00344 ( 40) SS BOND : angle 1.17993 ( 80) hydrogen bonds : bond 0.03755 ( 966) hydrogen bonds : angle 4.38770 ( 2685) link_BETA1-4 : bond 0.00556 ( 3) link_BETA1-4 : angle 1.12018 ( 9) link_NAG-ASN : bond 0.00307 ( 33) link_NAG-ASN : angle 1.59439 ( 99) *********************** 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 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6035 (mtp180) cc_final: 0.5733 (mmm-85) REVERT: A 166 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6969 (t) REVERT: A 319 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7247 (mmt180) REVERT: A 339 HIS cc_start: 0.7973 (t-90) cc_final: 0.7750 (t-170) REVERT: B 731 MET cc_start: 0.9352 (ptt) cc_final: 0.8973 (ptt) REVERT: B 1092 GLU cc_start: 0.8239 (pm20) cc_final: 0.7680 (pt0) REVERT: B 1138 TYR cc_start: 0.7733 (t80) cc_final: 0.7492 (t80) REVERT: C 459 SER cc_start: 0.8745 (p) cc_final: 0.8481 (t) REVERT: C 574 ASP cc_start: 0.8134 (t70) cc_final: 0.7816 (t0) outliers start: 34 outliers final: 16 residues processed: 219 average time/residue: 0.4501 time to fit residues: 118.0258 Evaluate side-chains 208 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 1128 VAL 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 B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN B 188 ASN B 207 HIS B 394 ASN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124727 restraints weight = 29400.568| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.66 r_work: 0.3151 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25540 Z= 0.121 Angle : 0.501 5.771 34829 Z= 0.260 Chirality : 0.044 0.305 4041 Planarity : 0.003 0.054 4434 Dihedral : 5.027 53.688 4098 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 1.22 % Allowed : 14.44 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 3081 helix: 2.15 (0.20), residues: 745 sheet: 0.47 (0.19), residues: 696 loop : -1.05 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.013 0.001 TYR A 421 PHE 0.024 0.001 PHE A 168 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00287 (25464) covalent geometry : angle 0.48956 (34641) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.37200 ( 80) hydrogen bonds : bond 0.04322 ( 966) hydrogen bonds : angle 4.42121 ( 2685) link_BETA1-4 : bond 0.00478 ( 3) link_BETA1-4 : angle 1.26762 ( 9) link_NAG-ASN : bond 0.00270 ( 33) link_NAG-ASN : angle 1.66759 ( 99) *********************** 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 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5722 (mmm-85) REVERT: A 166 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7025 (t) REVERT: B 458 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7442 (mtpt) REVERT: B 731 MET cc_start: 0.9360 (ptt) cc_final: 0.8992 (ptt) REVERT: B 1092 GLU cc_start: 0.8206 (pm20) cc_final: 0.7657 (pt0) REVERT: B 1138 TYR cc_start: 0.7784 (t80) cc_final: 0.7546 (t80) REVERT: C 459 SER cc_start: 0.8739 (p) cc_final: 0.8511 (t) REVERT: C 574 ASP cc_start: 0.8153 (t70) cc_final: 0.7833 (t0) REVERT: C 981 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8435 (mt) outliers start: 33 outliers final: 24 residues processed: 221 average time/residue: 0.4323 time to fit residues: 114.9434 Evaluate side-chains 219 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 392 PHE 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 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 532 ASN 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 1050 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 188 ASN B 207 HIS B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126698 restraints weight = 29417.187| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.68 r_work: 0.3149 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25540 Z= 0.105 Angle : 0.490 5.747 34829 Z= 0.255 Chirality : 0.044 0.308 4041 Planarity : 0.003 0.054 4434 Dihedral : 4.992 53.851 4098 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.18 % Allowed : 14.66 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3081 helix: 2.19 (0.20), residues: 745 sheet: 0.49 (0.19), residues: 694 loop : -1.04 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.013 0.001 TYR C1067 PHE 0.025 0.001 PHE A 168 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00243 (25464) covalent geometry : angle 0.47871 (34641) SS BOND : bond 0.00359 ( 40) SS BOND : angle 1.28879 ( 80) hydrogen bonds : bond 0.04129 ( 966) hydrogen bonds : angle 4.38750 ( 2685) link_BETA1-4 : bond 0.00457 ( 3) link_BETA1-4 : angle 1.21997 ( 9) link_NAG-ASN : bond 0.00286 ( 33) link_NAG-ASN : angle 1.62835 ( 99) ********************** 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: 32 poor density : 198 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6068 (mtp180) cc_final: 0.5735 (mmm-85) REVERT: A 166 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7015 (t) REVERT: A 319 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7256 (mmt180) REVERT: A 869 MET cc_start: 0.8997 (mtt) cc_final: 0.8725 (mtt) REVERT: B 458 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7442 (mtpt) REVERT: B 731 MET cc_start: 0.9368 (ptt) cc_final: 0.9000 (ptt) REVERT: B 1092 GLU cc_start: 0.8256 (pm20) cc_final: 0.7669 (pt0) REVERT: B 1138 TYR cc_start: 0.7749 (t80) cc_final: 0.7509 (t80) REVERT: C 459 SER cc_start: 0.8727 (p) cc_final: 0.8496 (t) REVERT: C 574 ASP cc_start: 0.8162 (t70) cc_final: 0.7794 (t0) REVERT: C 981 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8419 (mt) outliers start: 32 outliers final: 26 residues processed: 220 average time/residue: 0.4460 time to fit residues: 118.2470 Evaluate side-chains 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 392 PHE 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 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 532 ASN 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 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 302 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 271 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 310 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 114 optimal weight: 0.2980 chunk 289 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 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 B 188 ASN B 207 HIS B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126442 restraints weight = 29243.434| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.66 r_work: 0.3163 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25540 Z= 0.101 Angle : 0.489 6.896 34829 Z= 0.254 Chirality : 0.043 0.302 4041 Planarity : 0.003 0.055 4434 Dihedral : 4.956 53.734 4098 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 1.03 % Allowed : 14.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3081 helix: 2.23 (0.20), residues: 745 sheet: 0.45 (0.19), residues: 710 loop : -0.99 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.013 0.001 TYR A1067 PHE 0.024 0.001 PHE A 168 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00231 (25464) covalent geometry : angle 0.47883 (34641) SS BOND : bond 0.00347 ( 40) SS BOND : angle 1.23016 ( 80) hydrogen bonds : bond 0.04033 ( 966) hydrogen bonds : angle 4.36458 ( 2685) link_BETA1-4 : bond 0.00466 ( 3) link_BETA1-4 : angle 1.19169 ( 9) link_NAG-ASN : bond 0.00288 ( 33) link_NAG-ASN : angle 1.60796 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5704.97 seconds wall clock time: 98 minutes 22.48 seconds (5902.48 seconds total)