Starting phenix.real_space_refine on Sat May 24 01:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0t_42869/05_2025/8v0t_42869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0t_42869/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0t_42869/05_2025/8v0t_42869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0t_42869/05_2025/8v0t_42869.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0t_42869/05_2025/8v0t_42869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0t_42869/05_2025/8v0t_42869.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.19, per 1000 atoms: 0.61 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: 6.59 Conformation dependent library (CDL) restraints added in 3.3 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 25.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 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: 10.86 Time building geometry restraints manager: 7.60 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: 0.08 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 58.060 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 66.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (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 TRP 0.057 0.003 TRP A 64 HIS 0.009 0.001 HIS C 207 PHE 0.046 0.003 PHE C 906 TYR 0.042 0.002 TYR B 170 ARG 0.009 0.001 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 27) link_NAG-ASN : angle 3.20179 ( 81) hydrogen bonds : bond 0.21235 ( 884) hydrogen bonds : angle 7.91570 ( 2445) SS BOND : bond 0.00510 ( 41) SS BOND : angle 1.90531 ( 82) covalent geometry : bond 0.00590 (25338) covalent geometry : angle 0.82263 (34470) *********************** 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 : 2.685 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: 0.4592 (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: 0.3180 time to fit residues: 111.4058 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 : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.0870 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.203629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128392 restraints weight = 29861.771| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.12 r_work: 0.3258 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 25406 Z= 0.110 Angle : 0.533 11.860 34633 Z= 0.277 Chirality : 0.044 0.235 3996 Planarity : 0.004 0.059 4425 Dihedral : 6.237 57.851 3909 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 0.41 % Allowed : 5.45 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3081 helix: 1.12 (0.19), residues: 706 sheet: -0.22 (0.20), residues: 618 loop : -1.57 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 64 HIS 0.003 0.001 HIS B 49 PHE 0.016 0.001 PHE C 906 TYR 0.020 0.001 TYR B 170 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 27) link_NAG-ASN : angle 2.36300 ( 81) hydrogen bonds : bond 0.04981 ( 884) hydrogen bonds : angle 5.41118 ( 2445) SS BOND : bond 0.00309 ( 41) SS BOND : angle 1.29314 ( 82) covalent geometry : bond 0.00247 (25338) covalent geometry : angle 0.51780 (34470) *********************** 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 210 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PRO cc_start: 0.8210 (Cg_endo) cc_final: 0.8002 (Cg_exo) REVERT: A 979 ASP cc_start: 0.8031 (m-30) cc_final: 0.7700 (m-30) REVERT: B 203 ILE cc_start: 0.6217 (mt) cc_final: 0.6010 (mt) REVERT: B 388 ASN cc_start: 0.8395 (m110) cc_final: 0.8193 (t0) REVERT: B 904 TYR cc_start: 0.7984 (m-10) cc_final: 0.6934 (m-10) REVERT: B 1084 ASP cc_start: 0.8156 (t70) cc_final: 0.7560 (t0) outliers start: 11 outliers final: 6 residues processed: 205 average time/residue: 0.3102 time to fit residues: 107.6350 Evaluate side-chains 188 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 437 ASN B 487 ASN B 556 ASN B 955 ASN B1010 GLN C 134 GLN C 321 GLN C 409 GLN C 564 GLN C 762 GLN C 913 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116546 restraints weight = 29818.848| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.56 r_work: 0.3228 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25406 Z= 0.275 Angle : 0.671 11.314 34633 Z= 0.345 Chirality : 0.049 0.290 3996 Planarity : 0.005 0.053 4425 Dihedral : 6.443 58.954 3909 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 1.33 % Allowed : 8.95 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3081 helix: 1.20 (0.20), residues: 697 sheet: -0.46 (0.20), residues: 646 loop : -1.70 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 64 HIS 0.007 0.001 HIS A1064 PHE 0.043 0.002 PHE A 906 TYR 0.017 0.002 TYR C 204 ARG 0.007 0.001 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 27) link_NAG-ASN : angle 2.71110 ( 81) hydrogen bonds : bond 0.06875 ( 884) hydrogen bonds : angle 5.36505 ( 2445) SS BOND : bond 0.00470 ( 41) SS BOND : angle 1.92325 ( 82) covalent geometry : bond 0.00683 (25338) covalent geometry : angle 0.65261 (34470) *********************** 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 225 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6328 (tt) cc_final: 0.6072 (tt) REVERT: A 979 ASP cc_start: 0.8190 (m-30) cc_final: 0.7892 (m-30) REVERT: A 1002 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7683 (tt0) REVERT: B 170 TYR cc_start: 0.7081 (t80) cc_final: 0.6652 (t80) REVERT: B 203 ILE cc_start: 0.6475 (mt) cc_final: 0.6247 (mt) REVERT: B 556 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7130 (p0) REVERT: B 663 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (t0) REVERT: C 114 THR cc_start: 0.3870 (OUTLIER) cc_final: 0.3662 (m) REVERT: C 140 PHE cc_start: 0.6429 (p90) cc_final: 0.6078 (p90) REVERT: C 1002 GLN cc_start: 0.8495 (tp40) cc_final: 0.7991 (tt0) outliers start: 36 outliers final: 25 residues processed: 211 average time/residue: 0.2969 time to fit residues: 106.4218 Evaluate side-chains 201 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE 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 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 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1100 THR 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 307 THR 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 128 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 277 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 239 GLN B 556 ASN B 762 GLN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 409 GLN C 762 GLN C 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.198827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126142 restraints weight = 29652.001| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.94 r_work: 0.3234 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25406 Z= 0.119 Angle : 0.533 12.218 34633 Z= 0.275 Chirality : 0.045 0.252 3996 Planarity : 0.004 0.052 4425 Dihedral : 5.952 59.193 3909 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.47 % Allowed : 10.94 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3081 helix: 1.73 (0.20), residues: 699 sheet: -0.31 (0.20), residues: 637 loop : -1.56 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.004 0.001 HIS B 49 PHE 0.020 0.001 PHE B 400 TYR 0.015 0.001 TYR C 37 ARG 0.004 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 2.39009 ( 81) hydrogen bonds : bond 0.04936 ( 884) hydrogen bonds : angle 4.92142 ( 2445) SS BOND : bond 0.00342 ( 41) SS BOND : angle 1.50660 ( 82) covalent geometry : bond 0.00274 (25338) covalent geometry : angle 0.51676 (34470) *********************** 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 232 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.7188 (tptt) cc_final: 0.6894 (tptp) REVERT: A 979 ASP cc_start: 0.7969 (m-30) cc_final: 0.7648 (m-30) REVERT: B 388 ASN cc_start: 0.8973 (t0) cc_final: 0.8360 (m110) REVERT: C 84 LEU cc_start: 0.7704 (mp) cc_final: 0.7329 (mp) REVERT: C 105 ILE cc_start: 0.9017 (mm) cc_final: 0.8802 (mm) REVERT: C 140 PHE cc_start: 0.6389 (p90) cc_final: 0.6012 (p90) REVERT: C 339 HIS cc_start: 0.4155 (OUTLIER) cc_final: 0.3558 (p90) REVERT: C 585 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5543 (pp) outliers start: 40 outliers final: 24 residues processed: 218 average time/residue: 0.3129 time to fit residues: 114.7277 Evaluate side-chains 204 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU 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 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 176 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 1010 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 339 HIS 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 705 VAL Chi-restraints excluded: chain C residue 994 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 227 optimal weight: 0.9980 chunk 277 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.0370 chunk 185 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- 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 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 239 GLN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 409 GLN C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.198555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122616 restraints weight = 30014.622| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.00 r_work: 0.3227 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25406 Z= 0.147 Angle : 0.545 12.026 34633 Z= 0.281 Chirality : 0.045 0.253 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.744 58.897 3909 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 1.73 % Allowed : 11.34 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3081 helix: 1.83 (0.20), residues: 699 sheet: -0.24 (0.20), residues: 629 loop : -1.58 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.018 0.001 PHE B 400 TYR 0.021 0.001 TYR B 170 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 2.40121 ( 81) hydrogen bonds : bond 0.05109 ( 884) hydrogen bonds : angle 4.83039 ( 2445) SS BOND : bond 0.00343 ( 41) SS BOND : angle 1.59193 ( 82) covalent geometry : bond 0.00354 (25338) covalent geometry : angle 0.52774 (34470) *********************** 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 236 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 2.498 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6601 (m-70) cc_final: 0.6134 (m170) REVERT: A 277 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 424 LYS cc_start: 0.7270 (tptt) cc_final: 0.7001 (tptp) REVERT: A 537 LYS cc_start: 0.6472 (mttm) cc_final: 0.6269 (mtpp) REVERT: A 979 ASP cc_start: 0.8025 (m-30) cc_final: 0.7710 (m-30) REVERT: B 170 TYR cc_start: 0.7087 (t80) cc_final: 0.6578 (t80) REVERT: B 388 ASN cc_start: 0.8989 (t0) cc_final: 0.8377 (m110) REVERT: B 437 ASN cc_start: 0.5901 (p0) cc_final: 0.5321 (t0) REVERT: B 904 TYR cc_start: 0.8117 (m-10) cc_final: 0.6948 (m-10) REVERT: B 1043 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 84 LEU cc_start: 0.7776 (mp) cc_final: 0.7436 (mp) REVERT: C 105 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8827 (mm) REVERT: C 140 PHE cc_start: 0.6438 (p90) cc_final: 0.6030 (p90) REVERT: C 339 HIS cc_start: 0.4398 (OUTLIER) cc_final: 0.3671 (p90) REVERT: C 585 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5611 (pp) outliers start: 47 outliers final: 35 residues processed: 220 average time/residue: 0.3132 time to fit residues: 116.8367 Evaluate side-chains 219 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 2.674 ------------------------------------------------------------------------------- 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 754 LEU Chi-restraints excluded: chain A residue 762 GLN 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 320 VAL Chi-restraints excluded: chain B residue 377 PHE 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 762 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 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 105 ILE Chi-restraints excluded: chain C residue 207 HIS 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU 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 59 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 276 optimal weight: 0.0370 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125756 restraints weight = 29432.631| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.76 r_work: 0.3267 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25406 Z= 0.108 Angle : 0.509 12.390 34633 Z= 0.262 Chirality : 0.044 0.240 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.409 57.235 3909 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.88 % Allowed : 11.93 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3081 helix: 2.14 (0.20), residues: 697 sheet: -0.15 (0.20), residues: 631 loop : -1.51 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 PHE 0.028 0.001 PHE B 400 TYR 0.019 0.001 TYR B 170 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 27) link_NAG-ASN : angle 2.31676 ( 81) hydrogen bonds : bond 0.04426 ( 884) hydrogen bonds : angle 4.63977 ( 2445) SS BOND : bond 0.00302 ( 41) SS BOND : angle 1.28958 ( 82) covalent geometry : bond 0.00248 (25338) covalent geometry : angle 0.49415 (34470) *********************** 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 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6477 (m-70) cc_final: 0.6090 (m170) REVERT: A 190 ARG cc_start: 0.7280 (mpt-90) cc_final: 0.7075 (mmt90) REVERT: A 277 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 424 LYS cc_start: 0.7284 (tptt) cc_final: 0.7011 (tptp) REVERT: A 564 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7281 (mm110) REVERT: A 979 ASP cc_start: 0.7945 (m-30) cc_final: 0.7613 (m-30) REVERT: B 170 TYR cc_start: 0.7034 (t80) cc_final: 0.6509 (t80) REVERT: B 388 ASN cc_start: 0.8969 (t0) cc_final: 0.8345 (m110) REVERT: B 437 ASN cc_start: 0.5957 (p0) cc_final: 0.5347 (t0) REVERT: B 904 TYR cc_start: 0.8083 (m-10) cc_final: 0.6924 (m-10) REVERT: C 84 LEU cc_start: 0.7734 (mp) cc_final: 0.7372 (mp) REVERT: C 105 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8815 (mm) REVERT: C 140 PHE cc_start: 0.6467 (p90) cc_final: 0.6043 (p90) REVERT: C 177 MET cc_start: 0.3807 (mpp) cc_final: 0.3603 (mpp) REVERT: C 190 ARG cc_start: 0.3682 (tpt170) cc_final: 0.3429 (tpt170) REVERT: C 204 TYR cc_start: 0.7876 (m-80) cc_final: 0.7558 (m-80) REVERT: C 226 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8457 (tt) REVERT: C 339 HIS cc_start: 0.4327 (OUTLIER) cc_final: 0.3647 (p90) REVERT: C 569 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.5570 (mp) REVERT: C 646 ARG cc_start: 0.8421 (tmt-80) cc_final: 0.8097 (tmt-80) outliers start: 51 outliers final: 31 residues processed: 216 average time/residue: 0.3260 time to fit residues: 117.9223 Evaluate side-chains 208 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU 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 377 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 762 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 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 226 LEU 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 591 SER 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 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 220 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 44 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 overall best weight: 2.9394 ------------------------------------------------------------------------------- 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 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 804 GLN B 644 GLN B 955 ASN C 394 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.195357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123942 restraints weight = 29525.276| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.95 r_work: 0.3141 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25406 Z= 0.277 Angle : 0.667 11.423 34633 Z= 0.342 Chirality : 0.049 0.271 3996 Planarity : 0.004 0.048 4425 Dihedral : 5.985 53.215 3909 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 2.25 % Allowed : 12.01 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3081 helix: 1.59 (0.20), residues: 700 sheet: -0.50 (0.19), residues: 661 loop : -1.68 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.007 0.001 HIS C1064 PHE 0.030 0.002 PHE B 400 TYR 0.020 0.002 TYR C 204 ARG 0.005 0.001 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 27) link_NAG-ASN : angle 2.64429 ( 81) hydrogen bonds : bond 0.06617 ( 884) hydrogen bonds : angle 5.08177 ( 2445) SS BOND : bond 0.00548 ( 41) SS BOND : angle 2.41857 ( 82) covalent geometry : bond 0.00691 (25338) covalent geometry : angle 0.64529 (34470) *********************** 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 : 2.535 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6401 (m-70) cc_final: 0.5896 (m170) REVERT: A 277 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 301 CYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7837 (m) REVERT: A 424 LYS cc_start: 0.7234 (tptt) cc_final: 0.6978 (tppt) REVERT: A 902 MET cc_start: 0.8736 (mmt) cc_final: 0.8522 (mmt) REVERT: A 979 ASP cc_start: 0.7970 (m-30) cc_final: 0.7648 (m-30) REVERT: A 1002 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7314 (tt0) REVERT: B 53 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6924 (t0) REVERT: B 170 TYR cc_start: 0.6790 (t80) cc_final: 0.6371 (t80) REVERT: B 319 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6957 (ptp-110) REVERT: B 388 ASN cc_start: 0.9029 (t0) cc_final: 0.8391 (m110) REVERT: B 663 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8347 (t70) REVERT: C 105 ILE cc_start: 0.8971 (mm) cc_final: 0.8718 (mm) REVERT: C 140 PHE cc_start: 0.6603 (p90) cc_final: 0.6161 (p90) REVERT: C 177 MET cc_start: 0.3688 (mpp) cc_final: 0.3456 (mpp) REVERT: C 241 LEU cc_start: 0.8004 (mp) cc_final: 0.7792 (mt) REVERT: C 392 PHE cc_start: 0.7085 (m-80) cc_final: 0.6753 (m-80) REVERT: C 529 LYS cc_start: 0.6859 (ttmt) cc_final: 0.6320 (mttm) REVERT: C 569 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5667 (mp) REVERT: C 1002 GLN cc_start: 0.8237 (tp40) cc_final: 0.7712 (tt0) outliers start: 61 outliers final: 46 residues processed: 231 average time/residue: 0.3070 time to fit residues: 120.2913 Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 301 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 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 578 ASP Chi-restraints excluded: chain A residue 754 LEU 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 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 377 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 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 878 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 101 ILE Chi-restraints excluded: chain C residue 207 HIS 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 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 649 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.7980 chunk 58 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 308 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 564 GLN A 675 GLN B 196 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 992 GLN C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125644 restraints weight = 29585.244| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.08 r_work: 0.3212 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25406 Z= 0.105 Angle : 0.525 12.457 34633 Z= 0.270 Chirality : 0.045 0.322 3996 Planarity : 0.004 0.059 4425 Dihedral : 5.437 54.397 3909 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 1.62 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3081 helix: 2.04 (0.20), residues: 704 sheet: -0.27 (0.20), residues: 640 loop : -1.53 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS B 207 PHE 0.022 0.001 PHE B 400 TYR 0.017 0.001 TYR B 170 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 27) link_NAG-ASN : angle 2.31176 ( 81) hydrogen bonds : bond 0.04448 ( 884) hydrogen bonds : angle 4.66562 ( 2445) SS BOND : bond 0.00466 ( 41) SS BOND : angle 1.49401 ( 82) covalent geometry : bond 0.00236 (25338) covalent geometry : angle 0.50886 (34470) *********************** 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 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6311 (m-70) cc_final: 0.5796 (m170) REVERT: A 86 PHE cc_start: 0.6869 (t80) cc_final: 0.6603 (t80) REVERT: A 177 MET cc_start: 0.2326 (mtp) cc_final: 0.1647 (mpp) REVERT: A 277 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 301 CYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7720 (m) REVERT: A 424 LYS cc_start: 0.7282 (tptt) cc_final: 0.7041 (tppt) REVERT: A 514 SER cc_start: 0.7590 (OUTLIER) cc_final: 0.7335 (p) REVERT: A 564 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7175 (mm110) REVERT: A 979 ASP cc_start: 0.7998 (m-30) cc_final: 0.7681 (m-30) REVERT: B 170 TYR cc_start: 0.6749 (t80) cc_final: 0.6326 (t80) REVERT: B 388 ASN cc_start: 0.8997 (t0) cc_final: 0.8342 (m110) REVERT: B 515 PHE cc_start: 0.8563 (m-80) cc_final: 0.8331 (m-80) REVERT: B 586 ASP cc_start: 0.7727 (m-30) cc_final: 0.7423 (m-30) REVERT: B 663 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8350 (t0) REVERT: C 84 LEU cc_start: 0.7563 (mp) cc_final: 0.7174 (mp) REVERT: C 105 ILE cc_start: 0.8932 (mm) cc_final: 0.8712 (mm) REVERT: C 140 PHE cc_start: 0.6544 (p90) cc_final: 0.6097 (p90) REVERT: C 177 MET cc_start: 0.3984 (mpp) cc_final: 0.3763 (mpp) REVERT: C 224 GLU cc_start: 0.7804 (mp0) cc_final: 0.7578 (mp0) REVERT: C 392 PHE cc_start: 0.7012 (m-80) cc_final: 0.6678 (m-80) outliers start: 44 outliers final: 32 residues processed: 211 average time/residue: 0.3205 time to fit residues: 114.6909 Evaluate side-chains 211 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR 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 754 LEU 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 196 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 377 PHE 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 585 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 878 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 101 ILE Chi-restraints excluded: chain C residue 207 HIS 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 531 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 278 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 162 optimal weight: 0.0010 chunk 263 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 675 GLN B 196 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.199617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126265 restraints weight = 29771.544| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.14 r_work: 0.3229 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25406 Z= 0.103 Angle : 0.516 12.317 34633 Z= 0.265 Chirality : 0.044 0.274 3996 Planarity : 0.004 0.050 4425 Dihedral : 5.176 53.777 3909 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 1.51 % Allowed : 13.37 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3081 helix: 2.19 (0.20), residues: 705 sheet: -0.13 (0.20), residues: 605 loop : -1.50 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.001 PHE A 855 TYR 0.017 0.001 TYR B 170 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 27) link_NAG-ASN : angle 2.29238 ( 81) hydrogen bonds : bond 0.04299 ( 884) hydrogen bonds : angle 4.56927 ( 2445) SS BOND : bond 0.00298 ( 41) SS BOND : angle 1.40399 ( 82) covalent geometry : bond 0.00232 (25338) covalent geometry : angle 0.50061 (34470) *********************** 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 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6256 (m-70) cc_final: 0.5764 (m170) REVERT: A 86 PHE cc_start: 0.6867 (t80) cc_final: 0.6642 (t80) REVERT: A 277 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 424 LYS cc_start: 0.7298 (tptt) cc_final: 0.7059 (tppt) REVERT: A 514 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 564 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7106 (mm110) REVERT: A 979 ASP cc_start: 0.7949 (m-30) cc_final: 0.7633 (m-30) REVERT: B 170 TYR cc_start: 0.6737 (t80) cc_final: 0.6309 (t80) REVERT: B 388 ASN cc_start: 0.8984 (t0) cc_final: 0.8342 (m110) REVERT: B 437 ASN cc_start: 0.5071 (p0) cc_final: 0.4776 (t0) REVERT: B 515 PHE cc_start: 0.8546 (m-80) cc_final: 0.8343 (m-80) REVERT: B 586 ASP cc_start: 0.7714 (m-30) cc_final: 0.7407 (m-30) REVERT: B 663 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8345 (t0) REVERT: C 84 LEU cc_start: 0.7484 (mp) cc_final: 0.7073 (mp) REVERT: C 105 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (mm) REVERT: C 140 PHE cc_start: 0.6554 (p90) cc_final: 0.6103 (p90) REVERT: C 224 GLU cc_start: 0.7777 (mp0) cc_final: 0.7484 (mp0) REVERT: C 339 HIS cc_start: 0.4370 (OUTLIER) cc_final: 0.3519 (p-80) REVERT: C 392 PHE cc_start: 0.7013 (m-80) cc_final: 0.6676 (m-80) outliers start: 41 outliers final: 30 residues processed: 213 average time/residue: 0.3028 time to fit residues: 109.5733 Evaluate side-chains 217 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR 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 754 LEU 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 B residue 62 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 377 PHE 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 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE 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 105 ILE Chi-restraints excluded: chain C residue 207 HIS 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 531 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 130 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 242 optimal weight: 0.0020 chunk 56 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 303 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 A 675 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 992 GLN C 394 ASN 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 = 0.197725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123270 restraints weight = 29638.082| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.16 r_work: 0.3176 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2208 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= 0.146 Angle : 0.543 11.964 34633 Z= 0.278 Chirality : 0.045 0.279 3996 Planarity : 0.004 0.049 4425 Dihedral : 5.235 53.409 3909 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 1.51 % Allowed : 13.52 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3081 helix: 2.09 (0.20), residues: 700 sheet: -0.16 (0.20), residues: 632 loop : -1.52 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.027 0.001 PHE A 855 TYR 0.017 0.001 TYR B 170 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 27) link_NAG-ASN : angle 2.31883 ( 81) hydrogen bonds : bond 0.04827 ( 884) hydrogen bonds : angle 4.63291 ( 2445) SS BOND : bond 0.00331 ( 41) SS BOND : angle 1.61705 ( 82) covalent geometry : bond 0.00354 (25338) covalent geometry : angle 0.52638 (34470) ********************** 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 227 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6190 (m-70) cc_final: 0.5728 (m170) REVERT: A 86 PHE cc_start: 0.7075 (t80) cc_final: 0.6855 (t80) REVERT: A 277 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 301 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7734 (m) REVERT: A 424 LYS cc_start: 0.7299 (tptt) cc_final: 0.7053 (tppt) REVERT: A 514 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7327 (p) REVERT: A 564 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6970 (mm110) REVERT: A 979 ASP cc_start: 0.7957 (m-30) cc_final: 0.7631 (m-30) REVERT: B 170 TYR cc_start: 0.6775 (t80) cc_final: 0.6359 (t80) REVERT: B 388 ASN cc_start: 0.9001 (t0) cc_final: 0.8358 (m110) REVERT: B 515 PHE cc_start: 0.8589 (m-80) cc_final: 0.8371 (m-80) REVERT: B 586 ASP cc_start: 0.7747 (m-30) cc_final: 0.7386 (m-30) REVERT: B 663 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8352 (t0) REVERT: B 1043 CYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7592 (p) REVERT: C 84 LEU cc_start: 0.7601 (mp) cc_final: 0.7222 (mp) REVERT: C 105 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 140 PHE cc_start: 0.6710 (p90) cc_final: 0.6230 (p90) REVERT: C 357 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7548 (mtp180) REVERT: C 392 PHE cc_start: 0.7117 (m-80) cc_final: 0.6779 (m-80) REVERT: C 569 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5604 (mp) REVERT: C 646 ARG cc_start: 0.8567 (tmt-80) cc_final: 0.8214 (tmt-80) outliers start: 41 outliers final: 32 residues processed: 215 average time/residue: 0.3196 time to fit residues: 115.9925 Evaluate side-chains 225 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 392 PHE 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 754 LEU 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 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 377 PHE 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 762 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE 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 105 ILE Chi-restraints excluded: chain C residue 207 HIS 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 569 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 62 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 675 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.198824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121031 restraints weight = 29628.423| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.87 r_work: 0.3243 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25406 Z= 0.116 Angle : 0.521 12.137 34633 Z= 0.267 Chirality : 0.044 0.252 3996 Planarity : 0.004 0.049 4425 Dihedral : 5.140 53.656 3909 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.62 % Allowed : 13.41 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3081 helix: 2.17 (0.20), residues: 700 sheet: -0.10 (0.20), residues: 632 loop : -1.50 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS B 207 PHE 0.021 0.001 PHE A 855 TYR 0.017 0.001 TYR B 170 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 27) link_NAG-ASN : angle 2.28190 ( 81) hydrogen bonds : bond 0.04511 ( 884) hydrogen bonds : angle 4.56477 ( 2445) SS BOND : bond 0.00306 ( 41) SS BOND : angle 1.44222 ( 82) covalent geometry : bond 0.00271 (25338) covalent geometry : angle 0.50539 (34470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13915.23 seconds wall clock time: 240 minutes 49.42 seconds (14449.42 seconds total)