Starting phenix.real_space_refine on Mon Aug 25 03:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0t_42869/08_2025/8v0t_42869.map" } resolution = 3.1 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= 0.041 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 15822 2.51 5 N 4089 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s 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: 24777 Number of models: 1 Model: "" Number of chains: 6 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.10, per 1000 atoms: 0.25 Number of scatterers: 24777 At special positions: 0 Unit cell: (140.4, 130.68, 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 4752 8.00 N 4089 7.00 C 15822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 131 " - pdb=" SG CYS B 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 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 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 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 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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 51 sheets defined 25.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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 349 through 353 removed outlier: 4.173A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.777A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.910A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.035A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.750A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) 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: 3.846A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 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 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.508A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.717A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.536A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.702A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.570A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.629A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.767A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) 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: 3.846A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.676A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.591A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) 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: 3.663A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.549A 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: 3.651A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.694A 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 removed outlier: 3.522A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.943A 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 366 through 372 removed outlier: 3.707A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.720A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.013A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.858A pdb=" N SER C 443 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.778A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.505A 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: 3.677A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.641A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 removed outlier: 4.009A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.540A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.659A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.579A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.574A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.587A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.022A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.153A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.844A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.735A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.184A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.695A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.711A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.188A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.002A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.959A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.747A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.864A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.594A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.629A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.576A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.739A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.092A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.604A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 584 through 586 removed outlier: 6.392A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.033A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.632A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.394A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.575A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.798A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.070A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 193 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 208 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS C 206 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 205 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 207 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.584A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.265A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.236A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.053A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.869A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 removed outlier: 6.107A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.587A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 894 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7723 1.34 - 1.46: 6328 1.46 - 1.59: 11144 1.59 - 1.72: 2 1.72 - 1.84: 141 Bond restraints: 25338 Sorted by residual: bond pdb=" CA ASN A 196 " pdb=" CB ASN A 196 " ideal model delta sigma weight residual 1.527 1.641 -0.114 2.48e-02 1.63e+03 2.10e+01 bond pdb=" CB PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.52e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.12e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 33985 2.86 - 5.73: 422 5.73 - 8.59: 54 8.59 - 11.46: 5 11.46 - 14.32: 4 Bond angle restraints: 34470 Sorted by residual: angle pdb=" CA PRO A 209 " pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 112.00 98.90 13.10 1.40e+00 5.10e-01 8.75e+01 angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 120.33 124.67 -4.34 8.00e-01 1.56e+00 2.94e+01 angle pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" CD PRO C 82 " ideal model delta sigma weight residual 112.00 104.48 7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.09 117.45 -6.36 1.33e+00 5.65e-01 2.28e+01 angle pdb=" CG1 ILE C 128 " pdb=" CB ILE C 128 " pdb=" CG2 ILE C 128 " ideal model delta sigma weight residual 110.70 96.38 14.32 3.00e+00 1.11e-01 2.28e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 13906 18.06 - 36.12: 1283 36.12 - 54.17: 209 54.17 - 72.23: 54 72.23 - 90.29: 31 Dihedral angle restraints: 15483 sinusoidal: 6378 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -176.29 90.29 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 174.87 -81.87 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 146.97 -53.97 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 15480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3610 0.096 - 0.192: 357 0.192 - 0.288: 24 0.288 - 0.384: 4 0.384 - 0.480: 1 Chirality restraints: 3996 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 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB VAL B 511 " pdb=" CA VAL B 511 " pdb=" CG1 VAL B 511 " pdb=" CG2 VAL B 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB ILE C 128 " pdb=" CA ILE C 128 " pdb=" CG1 ILE C 128 " pdb=" CG2 ILE C 128 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3993 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.080 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 209 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " 0.065 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 82 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " 0.032 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP A 64 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.000 2.00e-02 2.50e+03 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7476 2.83 - 3.35: 20010 3.35 - 3.86: 39712 3.86 - 4.38: 43523 4.38 - 4.90: 79167 Nonbonded interactions: 189888 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.310 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.334 3.040 ... (remaining 189883 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.890 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.006 0.154 25406 Z= 0.252 Angle : 0.840 15.186 34633 Z= 0.442 Chirality : 0.057 0.480 3996 Planarity : 0.007 0.112 4425 Dihedral : 14.432 87.196 9498 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.03 % 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: -1.84 (0.14), residues: 3081 helix: -0.64 (0.17), residues: 698 sheet: -0.52 (0.20), residues: 613 loop : -1.76 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 646 TYR 0.042 0.002 TYR B 170 PHE 0.046 0.003 PHE C 906 TRP 0.057 0.003 TRP A 64 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00590 (25338) covalent geometry : angle 0.82263 (34470) SS BOND : bond 0.00510 ( 41) SS BOND : angle 1.90531 ( 82) hydrogen bonds : bond 0.21235 ( 884) hydrogen bonds : angle 7.91570 ( 2445) link_NAG-ASN : bond 0.00674 ( 27) link_NAG-ASN : angle 3.20179 ( 81) *********************** 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 209 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.7733 (Cg_exo) REVERT: A 902 MET cc_start: 0.8293 (mmt) cc_final: 0.8011 (mmt) REVERT: B 388 ASN cc_start: 0.8339 (m110) cc_final: 0.8115 (t0) REVERT: B 740 MET cc_start: 0.8071 (mmm) cc_final: 0.7758 (tpp) REVERT: B 904 TYR cc_start: 0.7889 (m-10) cc_final: 0.7000 (m-10) REVERT: B 1084 ASP cc_start: 0.7808 (t70) cc_final: 0.7448 (t0) REVERT: C 135 PHE cc_start: 0.4848 (m-10) cc_final: 0.4622 (m-10) REVERT: C 754 LEU cc_start: 0.8535 (mp) cc_final: 0.8267 (mt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1568 time to fit residues: 55.0121 Evaluate side-chains 166 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 955 ASN B1010 GLN C 66 HIS C 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.202604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126633 restraints weight = 30058.318| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.13 r_work: 0.3224 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25406 Z= 0.124 Angle : 0.546 11.847 34633 Z= 0.283 Chirality : 0.044 0.246 3996 Planarity : 0.004 0.059 4425 Dihedral : 6.279 56.857 3909 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 0.41 % Allowed : 5.78 % Favored : 93.81 % 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: -0.97 (0.14), residues: 3081 helix: 1.07 (0.19), residues: 706 sheet: -0.28 (0.20), residues: 645 loop : -1.57 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.019 0.001 TYR B 170 PHE 0.019 0.001 PHE C 906 TRP 0.028 0.001 TRP A 64 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00289 (25338) covalent geometry : angle 0.53028 (34470) SS BOND : bond 0.00498 ( 41) SS BOND : angle 1.38661 ( 82) hydrogen bonds : bond 0.05263 ( 884) hydrogen bonds : angle 5.43687 ( 2445) link_NAG-ASN : bond 0.00503 ( 27) link_NAG-ASN : angle 2.39983 ( 81) *********************** 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 206 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.8007 (Cg_exo) REVERT: A 979 ASP cc_start: 0.8057 (m-30) cc_final: 0.7726 (m-30) REVERT: B 203 ILE cc_start: 0.6198 (mt) cc_final: 0.5980 (mt) REVERT: B 388 ASN cc_start: 0.8403 (m110) cc_final: 0.8202 (t0) REVERT: B 904 TYR cc_start: 0.8029 (m-10) cc_final: 0.6973 (m-10) REVERT: B 1084 ASP cc_start: 0.8194 (t70) cc_final: 0.7600 (t0) outliers start: 11 outliers final: 7 residues processed: 201 average time/residue: 0.1516 time to fit residues: 51.8945 Evaluate side-chains 182 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 175 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 248 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 437 ASN B 487 ASN B 955 ASN B1010 GLN C 134 GLN C 564 GLN C 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.200550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129908 restraints weight = 29623.615| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.93 r_work: 0.3264 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25406 Z= 0.130 Angle : 0.529 11.777 34633 Z= 0.272 Chirality : 0.045 0.245 3996 Planarity : 0.004 0.054 4425 Dihedral : 5.837 54.060 3909 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 0.81 % Allowed : 8.10 % Favored : 91.09 % 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: -0.72 (0.15), residues: 3081 helix: 1.61 (0.20), residues: 706 sheet: -0.24 (0.20), residues: 635 loop : -1.52 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.013 0.001 TYR C 170 PHE 0.019 0.001 PHE A 906 TRP 0.025 0.001 TRP A 64 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00309 (25338) covalent geometry : angle 0.51367 (34470) SS BOND : bond 0.00325 ( 41) SS BOND : angle 1.31603 ( 82) hydrogen bonds : bond 0.04995 ( 884) hydrogen bonds : angle 4.99212 ( 2445) link_NAG-ASN : bond 0.00481 ( 27) link_NAG-ASN : angle 2.35482 ( 81) *********************** 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 207 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6241 (tt) cc_final: 0.5986 (tt) REVERT: A 979 ASP cc_start: 0.7979 (m-30) cc_final: 0.7656 (m-30) REVERT: B 203 ILE cc_start: 0.6095 (mt) cc_final: 0.5853 (mt) REVERT: B 904 TYR cc_start: 0.8030 (m-10) cc_final: 0.6920 (m-10) REVERT: C 114 THR cc_start: 0.3507 (OUTLIER) cc_final: 0.3277 (m) outliers start: 22 outliers final: 15 residues processed: 196 average time/residue: 0.1602 time to fit residues: 52.6266 Evaluate side-chains 186 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 268 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 chunk 213 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 955 ASN B1010 GLN C 321 GLN C 409 GLN C 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.198819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126335 restraints weight = 29462.826| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.94 r_work: 0.3240 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25406 Z= 0.149 Angle : 0.539 11.976 34633 Z= 0.278 Chirality : 0.045 0.246 3996 Planarity : 0.004 0.052 4425 Dihedral : 5.730 58.745 3909 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 1.29 % Allowed : 10.20 % Favored : 88.51 % 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: -0.65 (0.15), residues: 3081 helix: 1.77 (0.20), residues: 700 sheet: -0.22 (0.20), residues: 640 loop : -1.51 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.020 0.001 TYR B 170 PHE 0.026 0.001 PHE B 400 TRP 0.019 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00362 (25338) covalent geometry : angle 0.52362 (34470) SS BOND : bond 0.00404 ( 41) SS BOND : angle 1.42547 ( 82) hydrogen bonds : bond 0.05106 ( 884) hydrogen bonds : angle 4.88395 ( 2445) link_NAG-ASN : bond 0.00462 ( 27) link_NAG-ASN : angle 2.36967 ( 81) *********************** 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 218 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6603 (m-70) cc_final: 0.6238 (m170) REVERT: A 979 ASP cc_start: 0.8007 (m-30) cc_final: 0.7685 (m-30) REVERT: B 388 ASN cc_start: 0.8986 (t0) cc_final: 0.8371 (m110) REVERT: B 437 ASN cc_start: 0.5615 (p0) cc_final: 0.5319 (t0) REVERT: B 663 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8250 (t0) REVERT: B 904 TYR cc_start: 0.8107 (m-10) cc_final: 0.6975 (m-10) REVERT: C 105 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8883 (mm) REVERT: C 140 PHE cc_start: 0.6369 (p90) cc_final: 0.5975 (p90) REVERT: C 226 LEU cc_start: 0.8695 (tt) cc_final: 0.8445 (tt) REVERT: C 339 HIS cc_start: 0.4277 (OUTLIER) cc_final: 0.3460 (p90) outliers start: 35 outliers final: 22 residues processed: 206 average time/residue: 0.1538 time to fit residues: 53.5639 Evaluate side-chains 202 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 8.9990 chunk 190 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 245 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 955 ASN B1010 GLN C 409 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.198307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123642 restraints weight = 29511.216| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.73 r_work: 0.3262 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25406 Z= 0.143 Angle : 0.532 12.003 34633 Z= 0.275 Chirality : 0.045 0.246 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.437 53.740 3909 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.55 % Allowed : 10.83 % Favored : 87.62 % 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: -0.58 (0.15), residues: 3081 helix: 1.97 (0.20), residues: 699 sheet: -0.20 (0.20), residues: 631 loop : -1.52 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.014 0.001 TYR C1067 PHE 0.019 0.001 PHE B 400 TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (25338) covalent geometry : angle 0.51561 (34470) SS BOND : bond 0.00368 ( 41) SS BOND : angle 1.58943 ( 82) hydrogen bonds : bond 0.04962 ( 884) hydrogen bonds : angle 4.76648 ( 2445) link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 2.34452 ( 81) *********************** 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 231 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6535 (m-70) cc_final: 0.6125 (m170) REVERT: A 118 LEU cc_start: 0.7478 (tp) cc_final: 0.6522 (mp) REVERT: A 364 ASP cc_start: 0.5880 (t70) cc_final: 0.5361 (m-30) REVERT: A 424 LYS cc_start: 0.7228 (tptt) cc_final: 0.6926 (tptp) REVERT: A 537 LYS cc_start: 0.6582 (mttm) cc_final: 0.6327 (mtpp) REVERT: A 979 ASP cc_start: 0.8179 (m-30) cc_final: 0.7885 (m-30) REVERT: B 388 ASN cc_start: 0.9055 (t0) cc_final: 0.8438 (m110) REVERT: B 663 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8460 (t0) REVERT: B 904 TYR cc_start: 0.8222 (m-10) cc_final: 0.7064 (m-10) REVERT: B 1043 CYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7769 (p) REVERT: C 84 LEU cc_start: 0.7933 (mp) cc_final: 0.7545 (mp) REVERT: C 140 PHE cc_start: 0.6420 (p90) cc_final: 0.6004 (p90) REVERT: C 339 HIS cc_start: 0.4239 (OUTLIER) cc_final: 0.3658 (p90) REVERT: C 585 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5789 (pp) outliers start: 42 outliers final: 30 residues processed: 218 average time/residue: 0.1570 time to fit residues: 57.2381 Evaluate side-chains 211 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 257 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 644 GLN B 955 ASN B1010 GLN C 66 HIS C 409 GLN C 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126347 restraints weight = 29401.325| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.94 r_work: 0.3154 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25406 Z= 0.228 Angle : 0.618 11.559 34633 Z= 0.318 Chirality : 0.047 0.262 3996 Planarity : 0.004 0.049 4425 Dihedral : 5.728 52.932 3909 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 2.17 % Allowed : 11.42 % Favored : 86.41 % 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: -0.84 (0.15), residues: 3081 helix: 1.63 (0.20), residues: 700 sheet: -0.41 (0.20), residues: 667 loop : -1.62 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.022 0.001 TYR B 170 PHE 0.026 0.002 PHE A 906 TRP 0.017 0.001 TRP A 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00566 (25338) covalent geometry : angle 0.60030 (34470) SS BOND : bond 0.00454 ( 41) SS BOND : angle 1.90635 ( 82) hydrogen bonds : bond 0.06098 ( 884) hydrogen bonds : angle 4.98893 ( 2445) link_NAG-ASN : bond 0.00473 ( 27) link_NAG-ASN : angle 2.52701 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6453 (m-70) cc_final: 0.6030 (m170) REVERT: A 118 LEU cc_start: 0.7578 (tp) cc_final: 0.6586 (mp) REVERT: A 277 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8305 (mt) REVERT: A 364 ASP cc_start: 0.6203 (t70) cc_final: 0.5723 (m-30) REVERT: A 424 LYS cc_start: 0.7274 (tptt) cc_final: 0.7004 (tptp) REVERT: A 979 ASP cc_start: 0.8008 (m-30) cc_final: 0.7673 (m-30) REVERT: A 1002 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7418 (tt0) REVERT: B 170 TYR cc_start: 0.7025 (t80) cc_final: 0.6564 (t80) REVERT: B 319 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6886 (ptp-110) REVERT: B 388 ASN cc_start: 0.9037 (t0) cc_final: 0.8392 (m110) REVERT: B 437 ASN cc_start: 0.5859 (p0) cc_final: 0.5622 (p0) REVERT: B 663 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (t0) REVERT: C 140 PHE cc_start: 0.6386 (p90) cc_final: 0.5980 (p90) REVERT: C 339 HIS cc_start: 0.4357 (OUTLIER) cc_final: 0.3626 (p90) REVERT: C 529 LYS cc_start: 0.6828 (ttmt) cc_final: 0.6279 (mttm) REVERT: C 569 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5504 (mp) REVERT: C 585 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5419 (pp) REVERT: C 1002 GLN cc_start: 0.8240 (tp40) cc_final: 0.7744 (tt0) outliers start: 59 outliers final: 42 residues processed: 228 average time/residue: 0.1605 time to fit residues: 61.3139 Evaluate side-chains 222 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 196 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119028 restraints weight = 29628.008| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.10 r_work: 0.3177 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25406 Z= 0.197 Angle : 0.589 11.865 34633 Z= 0.303 Chirality : 0.047 0.262 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.664 53.305 3909 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 2.25 % Allowed : 11.82 % Favored : 85.93 % 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: -0.83 (0.15), residues: 3081 helix: 1.70 (0.20), residues: 699 sheet: -0.41 (0.19), residues: 663 loop : -1.65 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.020 0.001 TYR B 170 PHE 0.020 0.002 PHE C 86 TRP 0.015 0.001 TRP A 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00489 (25338) covalent geometry : angle 0.57206 (34470) SS BOND : bond 0.00388 ( 41) SS BOND : angle 1.73163 ( 82) hydrogen bonds : bond 0.05736 ( 884) hydrogen bonds : angle 4.90369 ( 2445) link_NAG-ASN : bond 0.00454 ( 27) link_NAG-ASN : angle 2.48152 ( 81) *********************** 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 245 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6371 (m-70) cc_final: 0.5861 (m170) REVERT: A 118 LEU cc_start: 0.7608 (tp) cc_final: 0.6583 (mp) REVERT: A 190 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.7060 (mmt90) REVERT: A 277 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 424 LYS cc_start: 0.7295 (tptt) cc_final: 0.7032 (tptp) REVERT: A 564 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7315 (mm110) REVERT: A 979 ASP cc_start: 0.7949 (m-30) cc_final: 0.7627 (m-30) REVERT: A 1002 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7424 (tt0) REVERT: B 170 TYR cc_start: 0.6818 (t80) cc_final: 0.6421 (t80) REVERT: B 319 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6873 (ptp-110) REVERT: B 388 ASN cc_start: 0.9028 (t0) cc_final: 0.8380 (m110) REVERT: B 437 ASN cc_start: 0.5883 (p0) cc_final: 0.5662 (p0) REVERT: B 663 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8351 (t0) REVERT: B 1043 CYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7691 (p) REVERT: C 140 PHE cc_start: 0.6588 (p90) cc_final: 0.6136 (p90) REVERT: C 529 LYS cc_start: 0.6819 (ttmt) cc_final: 0.6274 (mttm) REVERT: C 585 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5409 (pp) REVERT: C 1002 GLN cc_start: 0.8231 (tp40) cc_final: 0.7741 (tt0) outliers start: 61 outliers final: 46 residues processed: 226 average time/residue: 0.1533 time to fit residues: 58.1947 Evaluate side-chains 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 135 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 127 optimal weight: 0.0020 chunk 41 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 196 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118064 restraints weight = 29645.031| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.05 r_work: 0.3185 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25406 Z= 0.165 Angle : 0.565 12.033 34633 Z= 0.290 Chirality : 0.046 0.258 3996 Planarity : 0.004 0.051 4425 Dihedral : 5.566 53.523 3909 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 2.10 % Allowed : 12.08 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 694 sheet: -0.35 (0.19), residues: 661 loop : -1.63 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.019 0.001 TYR B 170 PHE 0.018 0.001 PHE B 400 TRP 0.014 0.001 TRP A 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00404 (25338) covalent geometry : angle 0.54771 (34470) SS BOND : bond 0.00364 ( 41) SS BOND : angle 1.62809 ( 82) hydrogen bonds : bond 0.05388 ( 884) hydrogen bonds : angle 4.83609 ( 2445) link_NAG-ASN : bond 0.00450 ( 27) link_NAG-ASN : angle 2.44236 ( 81) *********************** 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 236 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6355 (m-70) cc_final: 0.5860 (m170) REVERT: A 118 LEU cc_start: 0.7548 (tp) cc_final: 0.6403 (mp) REVERT: A 277 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8288 (mt) REVERT: A 424 LYS cc_start: 0.7294 (tptt) cc_final: 0.7046 (tppt) REVERT: A 979 ASP cc_start: 0.7976 (m-30) cc_final: 0.7655 (m-30) REVERT: B 53 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6886 (t0) REVERT: B 170 TYR cc_start: 0.6826 (t80) cc_final: 0.6433 (t80) REVERT: B 319 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6849 (ptp-110) REVERT: B 388 ASN cc_start: 0.9019 (t0) cc_final: 0.8373 (m110) REVERT: B 663 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8343 (t0) REVERT: B 816 SER cc_start: 0.8806 (p) cc_final: 0.8600 (m) REVERT: B 1043 CYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7664 (p) REVERT: C 140 PHE cc_start: 0.6716 (p90) cc_final: 0.6247 (p90) REVERT: C 529 LYS cc_start: 0.6814 (ttmt) cc_final: 0.6281 (mttm) REVERT: C 569 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5353 (mp) REVERT: C 585 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5504 (pp) REVERT: C 1002 GLN cc_start: 0.8198 (tp40) cc_final: 0.7721 (tt0) outliers start: 57 outliers final: 47 residues processed: 222 average time/residue: 0.1493 time to fit residues: 56.2791 Evaluate side-chains 227 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 247 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120323 restraints weight = 29675.053| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.06 r_work: 0.3183 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25406 Z= 0.128 Angle : 0.538 12.237 34633 Z= 0.277 Chirality : 0.045 0.250 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.355 53.786 3909 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 1.99 % Allowed : 12.41 % 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: -0.60 (0.15), residues: 3081 helix: 2.00 (0.20), residues: 704 sheet: -0.25 (0.20), residues: 658 loop : -1.56 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.019 0.001 TYR B 170 PHE 0.016 0.001 PHE B 400 TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00303 (25338) covalent geometry : angle 0.52168 (34470) SS BOND : bond 0.00328 ( 41) SS BOND : angle 1.49218 ( 82) hydrogen bonds : bond 0.04861 ( 884) hydrogen bonds : angle 4.70808 ( 2445) link_NAG-ASN : bond 0.00450 ( 27) link_NAG-ASN : angle 2.36500 ( 81) *********************** 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 239 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6342 (m-70) cc_final: 0.5858 (m170) REVERT: A 86 PHE cc_start: 0.6894 (t80) cc_final: 0.6660 (t80) REVERT: A 177 MET cc_start: 0.2425 (mtp) cc_final: 0.1743 (mpp) REVERT: A 277 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 424 LYS cc_start: 0.7283 (tptt) cc_final: 0.7040 (tppt) REVERT: A 979 ASP cc_start: 0.7991 (m-30) cc_final: 0.7698 (m-30) REVERT: B 53 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6861 (t0) REVERT: B 170 TYR cc_start: 0.6754 (t80) cc_final: 0.6357 (t80) REVERT: B 388 ASN cc_start: 0.9006 (t0) cc_final: 0.8356 (m110) REVERT: B 663 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8351 (t0) REVERT: B 1043 CYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7575 (p) REVERT: C 140 PHE cc_start: 0.6711 (p90) cc_final: 0.6233 (p90) REVERT: C 204 TYR cc_start: 0.7896 (m-80) cc_final: 0.7510 (m-80) REVERT: C 529 LYS cc_start: 0.6781 (ttmt) cc_final: 0.6251 (mttm) REVERT: C 585 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5390 (pp) outliers start: 54 outliers final: 44 residues processed: 222 average time/residue: 0.1488 time to fit residues: 56.3238 Evaluate side-chains 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.198427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124787 restraints weight = 29797.996| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.07 r_work: 0.3194 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25406 Z= 0.116 Angle : 0.535 12.287 34633 Z= 0.274 Chirality : 0.044 0.244 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.229 53.795 3909 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 1.66 % Allowed : 13.00 % Favored : 85.34 % 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: -0.50 (0.15), residues: 3081 helix: 2.11 (0.20), residues: 705 sheet: -0.16 (0.20), residues: 631 loop : -1.51 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.019 0.001 TYR B 170 PHE 0.015 0.001 PHE B 400 TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00268 (25338) covalent geometry : angle 0.51694 (34470) SS BOND : bond 0.00350 ( 41) SS BOND : angle 1.80016 ( 82) hydrogen bonds : bond 0.04576 ( 884) hydrogen bonds : angle 4.65232 ( 2445) link_NAG-ASN : bond 0.00449 ( 27) link_NAG-ASN : angle 2.32166 ( 81) ********************** 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 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6192 (m-70) cc_final: 0.5702 (m170) REVERT: A 86 PHE cc_start: 0.6920 (t80) cc_final: 0.6710 (t80) REVERT: A 118 LEU cc_start: 0.7178 (tt) cc_final: 0.5843 (mp) REVERT: A 177 MET cc_start: 0.2383 (mtp) cc_final: 0.1713 (mpp) REVERT: A 277 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 424 LYS cc_start: 0.7294 (tptt) cc_final: 0.7049 (tppt) REVERT: A 514 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7293 (p) REVERT: A 979 ASP cc_start: 0.7942 (m-30) cc_final: 0.7632 (m-30) REVERT: B 53 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6882 (t0) REVERT: B 170 TYR cc_start: 0.6754 (t80) cc_final: 0.6364 (t80) REVERT: B 388 ASN cc_start: 0.8999 (t0) cc_final: 0.8353 (m110) REVERT: B 515 PHE cc_start: 0.8547 (m-80) cc_final: 0.8339 (m-80) REVERT: B 904 TYR cc_start: 0.8065 (m-10) cc_final: 0.6954 (m-10) REVERT: C 84 LEU cc_start: 0.7464 (mp) cc_final: 0.7077 (mp) REVERT: C 140 PHE cc_start: 0.6730 (p90) cc_final: 0.6248 (p90) REVERT: C 204 TYR cc_start: 0.7910 (m-80) cc_final: 0.7532 (m-80) REVERT: C 339 HIS cc_start: 0.4443 (OUTLIER) cc_final: 0.3540 (p-80) REVERT: C 529 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6219 (mttm) outliers start: 45 outliers final: 39 residues processed: 215 average time/residue: 0.1493 time to fit residues: 54.7171 Evaluate side-chains 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 292 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120233 restraints weight = 29268.934| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.54 r_work: 0.3249 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25406 Z= 0.127 Angle : 0.538 12.100 34633 Z= 0.275 Chirality : 0.044 0.242 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.172 53.476 3909 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.84 % Allowed : 12.97 % Favored : 85.19 % 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: -0.49 (0.15), residues: 3081 helix: 2.12 (0.20), residues: 705 sheet: -0.13 (0.20), residues: 639 loop : -1.53 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.019 0.001 TYR B 170 PHE 0.016 0.001 PHE C 392 TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (25338) covalent geometry : angle 0.52095 (34470) SS BOND : bond 0.00318 ( 41) SS BOND : angle 1.66968 ( 82) hydrogen bonds : bond 0.04677 ( 884) hydrogen bonds : angle 4.62519 ( 2445) link_NAG-ASN : bond 0.00445 ( 27) link_NAG-ASN : angle 2.31415 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7689.45 seconds wall clock time: 132 minutes 22.02 seconds (7942.02 seconds total)