Starting phenix.real_space_refine on Sun May 25 02:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.map" model { file = "/net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uum_42590/05_2025/8uum_42590.cif" } resolution = 3.9 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= 0.016 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 116 5.16 5 C 16436 2.51 5 N 4252 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25786 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 8475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8475 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 5 Chain: "A" Number of atoms: 8465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8465 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8441 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 57, 'TRANS': 1023} Chain breaks: 5 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 16.17, per 1000 atoms: 0.63 Number of scatterers: 25786 At special positions: 0 Unit cell: (146.08, 156.704, 200.971, 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 116 16.00 O 4982 8.00 N 4252 7.00 C 16436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=1, symmetry=0 Links applied ALPHA1-4 " NAG D 1 " - " MAN D 2 " " NAG E 1 " - " MAN E 2 " " NAG F 1 " - " MAN F 2 " " NAG G 1 " - " MAN G 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1307 " - " ASN A 709 " " NAG B1302 " - " ASN B1134 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 801 " " NAG B1309 " - " ASN B 61 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 3.5 seconds 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6082 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 24.3% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.612A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.060A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.216A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.561A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.541A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.788A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.983A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.600A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) 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: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.700A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.525A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.615A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.640A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.744A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.590A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 4.435A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.585A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.169A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.416A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.570A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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: 3.777A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.517A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.899A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.582A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.998A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.593A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.815A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.159A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.601A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.436A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.537A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' 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: 3.548A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.947A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.691A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.543A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.571A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.678A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 982 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.198A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.772A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.434A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.834A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.226A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.240A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.221A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.220A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.593A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.395A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.881A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.008A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.885A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS A 69 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY A 261 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.195A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.676A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 133 through 143 removed outlier: 8.746A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.609A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.717A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.507A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.355A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.823A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.450A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.102A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.915A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.622A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.838A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 989 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 8.01 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: 7954 1.34 - 1.46: 6777 1.46 - 1.59: 11506 1.59 - 1.72: 0 1.72 - 1.85: 146 Bond restraints: 26383 Sorted by residual: bond pdb=" C LYS C 790 " pdb=" N THR C 791 " ideal model delta sigma weight residual 1.329 1.209 0.120 1.86e-02 2.89e+03 4.18e+01 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.335 1.415 -0.080 1.28e-02 6.10e+03 3.95e+01 bond pdb=" CA GLN B 965 " pdb=" C GLN B 965 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.41e-02 5.03e+03 1.73e+01 bond pdb=" C5 MAN E 2 " pdb=" O5 MAN E 2 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.30e-02 5.92e+03 7.07e+00 ... (remaining 26378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 34597 2.49 - 4.97: 1177 4.97 - 7.46: 113 7.46 - 9.94: 21 9.94 - 12.43: 6 Bond angle restraints: 35914 Sorted by residual: angle pdb=" C ARG C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta sigma weight residual 122.18 117.47 4.71 6.90e-01 2.10e+00 4.67e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.40 -6.70 1.22e+00 6.72e-01 3.01e+01 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C VAL A 781 " pdb=" N PHE A 782 " pdb=" CA PHE A 782 " ideal model delta sigma weight residual 122.79 114.13 8.66 1.70e+00 3.46e-01 2.60e+01 angle pdb=" C LEU A 945 " pdb=" N GLY A 946 " pdb=" CA GLY A 946 " ideal model delta sigma weight residual 120.03 125.55 -5.52 1.12e+00 7.97e-01 2.43e+01 ... (remaining 35909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 15190 23.80 - 47.60: 788 47.60 - 71.41: 98 71.41 - 95.21: 31 95.21 - 119.01: 22 Dihedral angle restraints: 16129 sinusoidal: 6677 harmonic: 9452 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.41 76.59 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual 180.00 140.77 39.23 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3571 0.089 - 0.178: 533 0.178 - 0.267: 26 0.267 - 0.356: 2 0.356 - 0.445: 3 Chirality restraints: 4135 Sorted by residual: chirality pdb=" CB ILE C1115 " pdb=" CA ILE C1115 " pdb=" CG1 ILE C1115 " pdb=" CG2 ILE C1115 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 4132 not shown) Planarity restraints: 4628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ALA A 958 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA A 958 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 959 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 956 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ALA A 956 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA A 956 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 957 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 956 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA B 956 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA B 956 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN B 957 " 0.019 2.00e-02 2.50e+03 ... (remaining 4625 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5452 2.77 - 3.30: 23277 3.30 - 3.84: 42243 3.84 - 4.37: 46355 4.37 - 4.90: 81472 Nonbonded interactions: 198799 Sorted by model distance: nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.241 3.040 nonbonded pdb=" O LEU A 296 " pdb=" OG1 THR A 299 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 307 " pdb=" OG1 THR B 602 " model vdw 2.254 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.267 3.040 ... (remaining 198794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 622 or resid 635 through 831 or resid 834 or re \ sid 852 through 1148 or resid 1302 through 1303)) selection = (chain 'B' and (resid 14 through 622 or resid 635 through 831 or resid 834 or re \ sid 852 through 1148 or resid 1303 through 1304)) selection = (chain 'C' and (resid 14 through 622 or resid 635 through 831 or resid 850 or re \ sid 852 through 1148 or resid 1302 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 4.640 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: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.440 Process input model: 62.160 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.008 0.123 26438 Z= 0.370 Angle : 1.046 12.429 36035 Z= 0.585 Chirality : 0.060 0.445 4135 Planarity : 0.007 0.073 4619 Dihedral : 14.963 119.012 9924 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.14 % Allowed : 0.81 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.14), residues: 3211 helix: -0.22 (0.19), residues: 674 sheet: -0.08 (0.19), residues: 684 loop : -1.99 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 258 HIS 0.011 0.002 HIS C 655 PHE 0.049 0.003 PHE C 906 TYR 0.047 0.003 TYR C 421 ARG 0.012 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 9) link_NAG-ASN : angle 3.68320 ( 27) link_ALPHA1-4 : bond 0.00608 ( 4) link_ALPHA1-4 : angle 2.64464 ( 12) hydrogen bonds : bond 0.14548 ( 977) hydrogen bonds : angle 7.18361 ( 2700) SS BOND : bond 0.00592 ( 41) SS BOND : angle 1.84696 ( 82) covalent geometry : bond 0.00774 (26383) covalent geometry : angle 1.03819 (35914) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 3.110 Fit side-chains REVERT: C 1050 MET cc_start: 0.8156 (ptp) cc_final: 0.7938 (ptp) REVERT: B 869 MET cc_start: 0.8941 (pmm) cc_final: 0.8577 (pmm) REVERT: B 947 LYS cc_start: 0.9066 (mppt) cc_final: 0.8401 (tppt) REVERT: B 1050 MET cc_start: 0.8234 (ptp) cc_final: 0.7910 (ptp) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.3628 time to fit residues: 40.5616 Evaluate side-chains 44 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1011 GLN A 14 GLN A 188 ASN A 613 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 239 GLN B 616 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.031655 restraints weight = 202008.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032740 restraints weight = 108093.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033469 restraints weight = 71849.086| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26438 Z= 0.142 Angle : 0.599 9.213 36035 Z= 0.313 Chirality : 0.044 0.325 4135 Planarity : 0.005 0.062 4619 Dihedral : 9.770 101.237 4097 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.54 % 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: -1.12 (0.14), residues: 3211 helix: 0.94 (0.21), residues: 677 sheet: 0.00 (0.19), residues: 677 loop : -1.77 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.003 0.001 HIS A1083 PHE 0.014 0.001 PHE C 168 TYR 0.020 0.001 TYR B 313 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 9) link_NAG-ASN : angle 2.44954 ( 27) link_ALPHA1-4 : bond 0.00840 ( 4) link_ALPHA1-4 : angle 2.60957 ( 12) hydrogen bonds : bond 0.05053 ( 977) hydrogen bonds : angle 5.76273 ( 2700) SS BOND : bond 0.00276 ( 41) SS BOND : angle 0.96425 ( 82) covalent geometry : bond 0.00302 (26383) covalent geometry : angle 0.59225 (35914) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 3.032 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8583 (t80) cc_final: 0.8248 (t80) REVERT: C 1005 GLN cc_start: 0.9496 (mm-40) cc_final: 0.9279 (mm-40) REVERT: A 614 ASP cc_start: 0.8827 (m-30) cc_final: 0.8492 (t0) REVERT: A 900 MET cc_start: 0.9192 (mmp) cc_final: 0.8973 (mmt) REVERT: B 855 PHE cc_start: 0.8061 (p90) cc_final: 0.7852 (p90) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.3188 time to fit residues: 35.6208 Evaluate side-chains 49 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 214 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.032306 restraints weight = 203164.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033393 restraints weight = 109922.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034122 restraints weight = 73426.111| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26438 Z= 0.121 Angle : 0.543 8.641 36035 Z= 0.280 Chirality : 0.043 0.278 4135 Planarity : 0.004 0.057 4619 Dihedral : 8.183 87.306 4097 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.53 % Allowed : 7.92 % Favored : 91.55 % 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: -0.77 (0.14), residues: 3211 helix: 1.60 (0.21), residues: 666 sheet: 0.04 (0.19), residues: 668 loop : -1.59 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.003 0.001 HIS B1083 PHE 0.013 0.001 PHE B 133 TYR 0.017 0.001 TYR B 369 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 2.09097 ( 27) link_ALPHA1-4 : bond 0.01714 ( 4) link_ALPHA1-4 : angle 2.48995 ( 12) hydrogen bonds : bond 0.04274 ( 977) hydrogen bonds : angle 5.22439 ( 2700) SS BOND : bond 0.00232 ( 41) SS BOND : angle 0.78485 ( 82) covalent geometry : bond 0.00261 (26383) covalent geometry : angle 0.53755 (35914) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8571 (t80) cc_final: 0.8297 (t80) REVERT: C 223 LEU cc_start: 0.9057 (mt) cc_final: 0.8708 (tp) REVERT: C 955 ASN cc_start: 0.9132 (m-40) cc_final: 0.8702 (p0) REVERT: A 614 ASP cc_start: 0.8790 (m-30) cc_final: 0.8500 (t0) REVERT: A 773 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 777 ASN cc_start: 0.8526 (m-40) cc_final: 0.8116 (m-40) REVERT: A 900 MET cc_start: 0.9173 (mmp) cc_final: 0.8971 (mmt) outliers start: 15 outliers final: 5 residues processed: 71 average time/residue: 0.3334 time to fit residues: 42.1968 Evaluate side-chains 54 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 258 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 0.0020 chunk 214 optimal weight: 9.9990 chunk 172 optimal weight: 0.3980 overall best weight: 3.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN A 146 HIS A 913 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 271 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.046345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031309 restraints weight = 208790.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032373 restraints weight = 111755.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033088 restraints weight = 74528.214| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26438 Z= 0.193 Angle : 0.581 8.794 36035 Z= 0.298 Chirality : 0.043 0.265 4135 Planarity : 0.004 0.054 4619 Dihedral : 7.755 83.554 4097 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.53 % Allowed : 9.82 % Favored : 89.65 % 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 (0.14), residues: 3211 helix: 1.59 (0.21), residues: 687 sheet: -0.04 (0.19), residues: 690 loop : -1.57 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.005 0.001 HIS B1083 PHE 0.014 0.001 PHE B 855 TYR 0.014 0.001 TYR C 612 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 9) link_NAG-ASN : angle 1.96999 ( 27) link_ALPHA1-4 : bond 0.01300 ( 4) link_ALPHA1-4 : angle 2.25442 ( 12) hydrogen bonds : bond 0.04352 ( 977) hydrogen bonds : angle 5.24427 ( 2700) SS BOND : bond 0.00296 ( 41) SS BOND : angle 0.85000 ( 82) covalent geometry : bond 0.00419 (26383) covalent geometry : angle 0.57693 (35914) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 3.074 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8637 (t80) cc_final: 0.8289 (t80) REVERT: C 613 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8352 (pp30) REVERT: C 869 MET cc_start: 0.9137 (mtt) cc_final: 0.8808 (ptp) REVERT: A 614 ASP cc_start: 0.8815 (m-30) cc_final: 0.8548 (t0) REVERT: A 773 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 777 ASN cc_start: 0.8522 (m-40) cc_final: 0.8032 (m-40) outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.3393 time to fit residues: 39.0004 Evaluate side-chains 57 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.046391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031442 restraints weight = 206763.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.032493 restraints weight = 112160.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033208 restraints weight = 75304.156| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26438 Z= 0.153 Angle : 0.546 8.531 36035 Z= 0.281 Chirality : 0.042 0.255 4135 Planarity : 0.004 0.052 4619 Dihedral : 7.125 80.755 4097 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.74 % Allowed : 10.63 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3211 helix: 1.73 (0.21), residues: 686 sheet: -0.01 (0.19), residues: 692 loop : -1.54 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.004 0.001 HIS C 655 PHE 0.012 0.001 PHE C 133 TYR 0.013 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 9) link_NAG-ASN : angle 1.92195 ( 27) link_ALPHA1-4 : bond 0.01236 ( 4) link_ALPHA1-4 : angle 2.08850 ( 12) hydrogen bonds : bond 0.04208 ( 977) hydrogen bonds : angle 5.11715 ( 2700) SS BOND : bond 0.00300 ( 41) SS BOND : angle 0.98398 ( 82) covalent geometry : bond 0.00333 (26383) covalent geometry : angle 0.54137 (35914) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 2.780 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8631 (t80) cc_final: 0.8286 (t80) REVERT: C 1019 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8426 (tpp80) REVERT: A 614 ASP cc_start: 0.8780 (m-30) cc_final: 0.8549 (t0) REVERT: A 773 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 777 ASN cc_start: 0.8504 (m-40) cc_final: 0.7962 (m-40) REVERT: A 900 MET cc_start: 0.9212 (mmm) cc_final: 0.8887 (mmt) outliers start: 21 outliers final: 12 residues processed: 68 average time/residue: 0.3170 time to fit residues: 39.7785 Evaluate side-chains 61 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 250 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN A 953 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.046843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.031875 restraints weight = 205562.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032959 restraints weight = 109635.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033689 restraints weight = 72881.609| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26438 Z= 0.125 Angle : 0.526 12.700 36035 Z= 0.269 Chirality : 0.042 0.243 4135 Planarity : 0.004 0.052 4619 Dihedral : 6.354 75.569 4097 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.84 % Allowed : 11.79 % Favored : 87.36 % 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: 3211 helix: 2.03 (0.21), residues: 673 sheet: 0.08 (0.20), residues: 656 loop : -1.45 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.003 0.001 HIS C 655 PHE 0.012 0.001 PHE B 133 TYR 0.013 0.001 TYR C1067 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 9) link_NAG-ASN : angle 1.83255 ( 27) link_ALPHA1-4 : bond 0.01072 ( 4) link_ALPHA1-4 : angle 2.29663 ( 12) hydrogen bonds : bond 0.03964 ( 977) hydrogen bonds : angle 4.92616 ( 2700) SS BOND : bond 0.00241 ( 41) SS BOND : angle 0.81973 ( 82) covalent geometry : bond 0.00276 (26383) covalent geometry : angle 0.52142 (35914) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8687 (t80) cc_final: 0.8470 (t80) REVERT: C 869 MET cc_start: 0.9174 (mtt) cc_final: 0.8915 (ptp) REVERT: A 614 ASP cc_start: 0.8791 (m-30) cc_final: 0.8590 (t0) REVERT: A 773 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 777 ASN cc_start: 0.8398 (m-40) cc_final: 0.7839 (m-40) REVERT: A 900 MET cc_start: 0.9133 (mmm) cc_final: 0.8707 (mmt) REVERT: B 298 GLU cc_start: 0.9486 (tt0) cc_final: 0.9225 (mt-10) outliers start: 24 outliers final: 17 residues processed: 75 average time/residue: 0.3157 time to fit residues: 42.8105 Evaluate side-chains 71 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 299 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031083 restraints weight = 209199.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032113 restraints weight = 113194.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.032806 restraints weight = 76002.691| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26438 Z= 0.223 Angle : 0.595 10.840 36035 Z= 0.303 Chirality : 0.043 0.243 4135 Planarity : 0.004 0.054 4619 Dihedral : 6.446 76.698 4097 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.09 % Allowed : 12.39 % Favored : 86.52 % 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: -0.60 (0.15), residues: 3211 helix: 1.93 (0.21), residues: 676 sheet: -0.03 (0.19), residues: 691 loop : -1.52 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.006 0.001 HIS C 655 PHE 0.017 0.001 PHE B 855 TYR 0.013 0.001 TYR A1067 ARG 0.007 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 9) link_NAG-ASN : angle 1.85991 ( 27) link_ALPHA1-4 : bond 0.00934 ( 4) link_ALPHA1-4 : angle 2.08043 ( 12) hydrogen bonds : bond 0.04277 ( 977) hydrogen bonds : angle 5.12450 ( 2700) SS BOND : bond 0.00326 ( 41) SS BOND : angle 0.90285 ( 82) covalent geometry : bond 0.00483 (26383) covalent geometry : angle 0.59071 (35914) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8732 (t80) cc_final: 0.8451 (t80) REVERT: C 869 MET cc_start: 0.9156 (mtt) cc_final: 0.8872 (ptp) REVERT: A 614 ASP cc_start: 0.8838 (m-30) cc_final: 0.8630 (t0) REVERT: A 773 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 777 ASN cc_start: 0.8498 (m-40) cc_final: 0.7937 (m-40) REVERT: A 900 MET cc_start: 0.9174 (mmm) cc_final: 0.8699 (mmt) REVERT: B 298 GLU cc_start: 0.9506 (tt0) cc_final: 0.9205 (mt-10) outliers start: 31 outliers final: 21 residues processed: 82 average time/residue: 0.3252 time to fit residues: 47.6605 Evaluate side-chains 73 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 52 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 304 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.046121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031249 restraints weight = 208386.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032302 restraints weight = 113756.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033001 restraints weight = 76206.214| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26438 Z= 0.175 Angle : 0.563 10.870 36035 Z= 0.288 Chirality : 0.042 0.244 4135 Planarity : 0.004 0.051 4619 Dihedral : 6.314 74.662 4097 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.06 % Allowed : 12.92 % Favored : 86.03 % 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: -0.59 (0.15), residues: 3211 helix: 1.99 (0.21), residues: 675 sheet: -0.03 (0.20), residues: 658 loop : -1.50 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.005 0.001 HIS C 655 PHE 0.018 0.001 PHE B 392 TYR 0.013 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 9) link_NAG-ASN : angle 1.84535 ( 27) link_ALPHA1-4 : bond 0.00858 ( 4) link_ALPHA1-4 : angle 2.20817 ( 12) hydrogen bonds : bond 0.04208 ( 977) hydrogen bonds : angle 5.05116 ( 2700) SS BOND : bond 0.00399 ( 41) SS BOND : angle 0.88916 ( 82) covalent geometry : bond 0.00383 (26383) covalent geometry : angle 0.55852 (35914) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8752 (t80) cc_final: 0.8455 (t80) REVERT: C 869 MET cc_start: 0.9148 (mtt) cc_final: 0.8863 (ptp) REVERT: A 773 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 777 ASN cc_start: 0.8471 (m-40) cc_final: 0.7905 (m-40) REVERT: A 900 MET cc_start: 0.9139 (mmm) cc_final: 0.8628 (mmt) REVERT: B 298 GLU cc_start: 0.9490 (tt0) cc_final: 0.9195 (mt-10) outliers start: 30 outliers final: 24 residues processed: 80 average time/residue: 0.3254 time to fit residues: 47.5960 Evaluate side-chains 75 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 266 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 309 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 282 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.046638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031664 restraints weight = 205049.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.032759 restraints weight = 109049.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033487 restraints weight = 72202.429| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26438 Z= 0.118 Angle : 0.522 10.319 36035 Z= 0.267 Chirality : 0.042 0.242 4135 Planarity : 0.004 0.051 4619 Dihedral : 5.940 69.119 4097 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.99 % Allowed : 13.13 % Favored : 85.89 % 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: -0.38 (0.15), residues: 3211 helix: 2.27 (0.21), residues: 669 sheet: 0.06 (0.20), residues: 659 loop : -1.38 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.003 0.001 HIS B1083 PHE 0.029 0.001 PHE B 515 TYR 0.014 0.001 TYR C1067 ARG 0.002 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 9) link_NAG-ASN : angle 1.81801 ( 27) link_ALPHA1-4 : bond 0.00767 ( 4) link_ALPHA1-4 : angle 2.31620 ( 12) hydrogen bonds : bond 0.03931 ( 977) hydrogen bonds : angle 4.86622 ( 2700) SS BOND : bond 0.00230 ( 41) SS BOND : angle 0.84667 ( 82) covalent geometry : bond 0.00263 (26383) covalent geometry : angle 0.51762 (35914) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8720 (t80) cc_final: 0.8443 (t80) REVERT: C 869 MET cc_start: 0.9167 (mtt) cc_final: 0.8885 (ptp) REVERT: A 773 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 777 ASN cc_start: 0.8371 (m-40) cc_final: 0.7865 (m-40) REVERT: A 900 MET cc_start: 0.9121 (mmm) cc_final: 0.8587 (mmt) REVERT: B 298 GLU cc_start: 0.9500 (tt0) cc_final: 0.9218 (mt-10) outliers start: 28 outliers final: 25 residues processed: 78 average time/residue: 0.3208 time to fit residues: 45.9789 Evaluate side-chains 76 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 165 optimal weight: 0.0870 chunk 208 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.032139 restraints weight = 205023.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.033254 restraints weight = 109340.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033994 restraints weight = 72327.505| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26438 Z= 0.096 Angle : 0.509 10.444 36035 Z= 0.261 Chirality : 0.042 0.246 4135 Planarity : 0.003 0.050 4619 Dihedral : 5.640 64.054 4097 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.92 % Allowed : 13.27 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3211 helix: 2.38 (0.21), residues: 669 sheet: 0.15 (0.20), residues: 663 loop : -1.34 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.002 0.000 HIS C 655 PHE 0.027 0.001 PHE B 515 TYR 0.014 0.001 TYR C1067 ARG 0.002 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 1.79311 ( 27) link_ALPHA1-4 : bond 0.00711 ( 4) link_ALPHA1-4 : angle 2.32009 ( 12) hydrogen bonds : bond 0.03751 ( 977) hydrogen bonds : angle 4.74647 ( 2700) SS BOND : bond 0.00218 ( 41) SS BOND : angle 0.77773 ( 82) covalent geometry : bond 0.00215 (26383) covalent geometry : angle 0.50468 (35914) Misc. bond : bond 0.00002 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 869 MET cc_start: 0.9144 (mtt) cc_final: 0.8849 (ptp) REVERT: A 740 MET cc_start: 0.9183 (ppp) cc_final: 0.8898 (tmm) REVERT: A 773 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 777 ASN cc_start: 0.8274 (m-40) cc_final: 0.7761 (m-40) REVERT: A 900 MET cc_start: 0.9112 (mmm) cc_final: 0.8590 (mmt) REVERT: B 298 GLU cc_start: 0.9497 (tt0) cc_final: 0.9216 (mt-10) outliers start: 26 outliers final: 24 residues processed: 81 average time/residue: 0.3158 time to fit residues: 46.9652 Evaluate side-chains 74 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 267 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 243 optimal weight: 0.0020 chunk 201 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.047163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032218 restraints weight = 205107.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033330 restraints weight = 109413.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034076 restraints weight = 72465.315| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26438 Z= 0.095 Angle : 0.509 10.325 36035 Z= 0.259 Chirality : 0.042 0.247 4135 Planarity : 0.003 0.050 4619 Dihedral : 5.419 59.285 4097 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.95 % Allowed : 13.41 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3211 helix: 2.40 (0.21), residues: 669 sheet: 0.23 (0.20), residues: 649 loop : -1.31 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.002 0.000 HIS A1083 PHE 0.038 0.001 PHE C 168 TYR 0.014 0.001 TYR C1067 ARG 0.002 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 9) link_NAG-ASN : angle 1.75230 ( 27) link_ALPHA1-4 : bond 0.00686 ( 4) link_ALPHA1-4 : angle 2.27598 ( 12) hydrogen bonds : bond 0.03688 ( 977) hydrogen bonds : angle 4.70547 ( 2700) SS BOND : bond 0.00214 ( 41) SS BOND : angle 0.76409 ( 82) covalent geometry : bond 0.00214 (26383) covalent geometry : angle 0.50423 (35914) Misc. bond : bond 0.00000 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7766.20 seconds wall clock time: 137 minutes 27.63 seconds (8247.63 seconds total)