Starting phenix.real_space_refine on Sun Jul 5 06:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_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_42590/07_2026/8uum_42590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.map" model { file = "/net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8uum_42590/07_2026/8uum_42590.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3 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: 3 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: 3 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: 3 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: 6 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: 4.97, per 1000 atoms: 0.19 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: 1.98 Conformation dependent library (CDL) restraints added in 854.4 milliseconds 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: 0.97 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: 5.03 Time building geometry restraints manager: 2.51 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 - 23.14: 15080 23.14 - 46.28: 816 46.28 - 69.41: 92 69.41 - 92.55: 34 92.55 - 115.69: 12 Dihedral angle restraints: 16034 sinusoidal: 6582 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 16031 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.490 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 14.396 115.690 9829 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG A 158 TYR 0.047 0.003 TYR C 421 PHE 0.049 0.003 PHE C 906 TRP 0.028 0.003 TRP C 258 HIS 0.011 0.002 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.37 (26383) covalent geometry : angle 1.03819 / 0.58 (35914) SS BOND : bond 0.00592 / 0.40 ( 41) SS BOND : angle 1.84696 / 1.27 ( 82) hydrogen bonds : bond 0.14548 / 9.56 ( 977) hydrogen bonds : angle 7.18361 / 5.02 ( 2700) Misc. bond : bond 0.00046 / 0.02 ( 1) link_ALPHA1-4 : bond 0.00608 / 0.31 ( 4) link_ALPHA1-4 : angle 2.64464 / 1.72 ( 12) link_NAG-ASN : bond 0.00596 / 0.30 ( 9) link_NAG-ASN : angle 3.68320 / 2.49 ( 27) *********************** 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 : 1.048 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: 0.1395 time to fit residues: 15.4189 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 : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN C 616 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1011 GLN A 14 GLN A 30 ASN A 188 ASN A 234 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.046982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.031936 restraints weight = 202612.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033021 restraints weight = 107576.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033737 restraints weight = 71407.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034252 restraints weight = 54269.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034574 restraints weight = 44794.029| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26438 Z= 0.133 Angle : 0.583 6.919 36035 Z= 0.307 Chirality : 0.044 0.324 4135 Planarity : 0.004 0.062 4619 Dihedral : 8.652 101.265 4002 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3211 helix: 0.98 (0.21), residues: 677 sheet: 0.03 (0.19), residues: 676 loop : -1.76 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.020 0.001 TYR B 369 PHE 0.015 0.001 PHE C 168 TRP 0.014 0.001 TRP C 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (26383) covalent geometry : angle 0.57678 / 0.31 (35914) SS BOND : bond 0.00269 / 0.18 ( 41) SS BOND : angle 0.94923 / 0.68 ( 82) hydrogen bonds : bond 0.04932 / 3.27 ( 977) hydrogen bonds : angle 5.70578 / 3.97 ( 2700) Misc. bond : bond 0.00017 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00308 / 0.15 ( 4) link_ALPHA1-4 : angle 2.53568 / 1.63 ( 12) link_NAG-ASN : bond 0.00243 / 0.11 ( 9) link_NAG-ASN : angle 2.40794 / 1.56 ( 27) *********************** 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 63 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8567 (t80) cc_final: 0.8229 (t80) REVERT: C 1005 GLN cc_start: 0.9521 (mm-40) cc_final: 0.9287 (mm-40) REVERT: A 614 ASP cc_start: 0.8785 (m-30) cc_final: 0.8480 (t0) REVERT: B 855 PHE cc_start: 0.8049 (p90) cc_final: 0.7827 (p90) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.1329 time to fit residues: 14.4840 Evaluate side-chains 50 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 613 GLN 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 37 optimal weight: 6.9990 chunk 290 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 222 optimal weight: 0.0370 chunk 314 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032895 restraints weight = 207475.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034029 restraints weight = 109078.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034795 restraints weight = 71834.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.035278 restraints weight = 54000.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035651 restraints weight = 44627.047| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26438 Z= 0.096 Angle : 0.523 6.978 36035 Z= 0.272 Chirality : 0.043 0.288 4135 Planarity : 0.004 0.057 4619 Dihedral : 7.746 94.180 4002 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.56 % Allowed : 7.32 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3211 helix: 1.58 (0.21), residues: 664 sheet: 0.16 (0.19), residues: 658 loop : -1.58 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.023 0.001 TYR C 612 PHE 0.015 0.001 PHE C 168 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.000 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (26383) covalent geometry : angle 0.51729 / 0.27 (35914) SS BOND : bond 0.00213 / 0.16 ( 41) SS BOND : angle 0.74257 / 0.51 ( 82) hydrogen bonds : bond 0.04191 / 2.79 ( 977) hydrogen bonds : angle 5.20280 / 3.62 ( 2700) Misc. bond : bond 0.00016 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00592 / 0.31 ( 4) link_ALPHA1-4 : angle 2.49650 / 1.64 ( 12) link_NAG-ASN : bond 0.00346 / 0.16 ( 9) link_NAG-ASN : angle 2.16570 / 1.39 ( 27) *********************** 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 77 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8580 (t80) cc_final: 0.8309 (t80) REVERT: C 223 LEU cc_start: 0.9011 (mt) cc_final: 0.8665 (tp) REVERT: C 955 ASN cc_start: 0.9157 (m-40) cc_final: 0.8643 (p0) REVERT: A 614 ASP cc_start: 0.8737 (m-30) cc_final: 0.8490 (t0) REVERT: A 773 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 777 ASN cc_start: 0.8475 (m-40) cc_final: 0.8047 (m-40) REVERT: B 855 PHE cc_start: 0.8041 (p90) cc_final: 0.7745 (p90) REVERT: B 869 MET cc_start: 0.8798 (pmm) cc_final: 0.8595 (pmm) outliers start: 16 outliers final: 5 residues processed: 74 average time/residue: 0.1320 time to fit residues: 17.6516 Evaluate side-chains 56 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 731 MET 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 316 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 228 optimal weight: 30.0000 chunk 175 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.046266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031179 restraints weight = 208282.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.032251 restraints weight = 112144.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032959 restraints weight = 74572.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033443 restraints weight = 56798.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033731 restraints weight = 47155.935| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26438 Z= 0.205 Angle : 0.587 7.721 36035 Z= 0.304 Chirality : 0.043 0.266 4135 Planarity : 0.004 0.057 4619 Dihedral : 7.706 94.266 4002 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.63 % Allowed : 9.50 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3211 helix: 1.57 (0.21), residues: 687 sheet: -0.03 (0.19), residues: 704 loop : -1.58 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.013 0.001 TYR B 313 PHE 0.015 0.001 PHE B 855 TRP 0.014 0.001 TRP C 258 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (26383) covalent geometry : angle 0.58266 / 0.30 (35914) SS BOND : bond 0.00306 / 0.21 ( 41) SS BOND : angle 0.86610 / 0.62 ( 82) hydrogen bonds : bond 0.04408 / 2.92 ( 977) hydrogen bonds : angle 5.27032 / 3.66 ( 2700) Misc. bond : bond 0.00034 / 0.02 ( 1) link_ALPHA1-4 : bond 0.00334 / 0.17 ( 4) link_ALPHA1-4 : angle 2.34426 / 1.61 ( 12) link_NAG-ASN : bond 0.00244 / 0.13 ( 9) link_NAG-ASN : angle 2.00319 / 1.33 ( 27) *********************** 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 70 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8622 (t80) cc_final: 0.8275 (t80) REVERT: C 869 MET cc_start: 0.9063 (mtt) cc_final: 0.8735 (ptp) REVERT: A 614 ASP cc_start: 0.8782 (m-30) cc_final: 0.8517 (t0) REVERT: A 773 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 777 ASN cc_start: 0.8536 (m-40) cc_final: 0.8045 (m-40) outliers start: 18 outliers final: 6 residues processed: 66 average time/residue: 0.1407 time to fit residues: 16.9265 Evaluate side-chains 56 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain A residue 130 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 861 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 16 optimal weight: 20.0000 chunk 186 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN C 616 ASN C 655 HIS ** 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 655 HIS ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030500 restraints weight = 209012.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.031544 restraints weight = 112797.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.032234 restraints weight = 75300.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032691 restraints weight = 57353.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032969 restraints weight = 47840.308| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 26438 Z= 0.243 Angle : 0.633 12.474 36035 Z= 0.326 Chirality : 0.043 0.255 4135 Planarity : 0.004 0.056 4619 Dihedral : 7.829 96.415 4002 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.95 % Allowed : 10.91 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3211 helix: 1.58 (0.21), residues: 680 sheet: -0.17 (0.19), residues: 696 loop : -1.64 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.016 0.002 TYR C 421 PHE 0.022 0.002 PHE B 855 TRP 0.016 0.002 TRP C 258 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (26383) covalent geometry : angle 0.62856 / 0.32 (35914) SS BOND : bond 0.00350 / 0.24 ( 41) SS BOND : angle 1.10322 / 0.81 ( 82) hydrogen bonds : bond 0.04689 / 3.09 ( 977) hydrogen bonds : angle 5.40413 / 3.73 ( 2700) Misc. bond : bond 0.00066 / 0.03 ( 1) link_ALPHA1-4 : bond 0.00413 / 0.21 ( 4) link_ALPHA1-4 : angle 2.31039 / 1.56 ( 12) link_NAG-ASN : bond 0.00296 / 0.15 ( 9) link_NAG-ASN : angle 1.96787 / 1.31 ( 27) *********************** 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 78 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8696 (t80) cc_final: 0.8438 (t80) REVERT: A 153 MET cc_start: 0.8154 (mpp) cc_final: 0.7887 (mpp) REVERT: A 614 ASP cc_start: 0.8755 (m-30) cc_final: 0.8510 (t0) REVERT: B 298 GLU cc_start: 0.9487 (tt0) cc_final: 0.9187 (mt-10) outliers start: 27 outliers final: 16 residues processed: 75 average time/residue: 0.1581 time to fit residues: 21.1131 Evaluate side-chains 65 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL 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 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 415 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 205 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 284 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 252 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 953 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.045389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030311 restraints weight = 210008.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031334 restraints weight = 113151.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.032041 restraints weight = 75411.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032504 restraints weight = 57218.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032800 restraints weight = 47706.134| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 26438 Z= 0.258 Angle : 0.641 9.933 36035 Z= 0.329 Chirality : 0.043 0.261 4135 Planarity : 0.004 0.057 4619 Dihedral : 7.793 97.470 4002 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.16 % Allowed : 12.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3211 helix: 1.58 (0.21), residues: 680 sheet: -0.26 (0.19), residues: 682 loop : -1.68 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.014 0.002 TYR B 313 PHE 0.019 0.001 PHE B 855 TRP 0.016 0.001 TRP C 258 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (26383) covalent geometry : angle 0.63610 / 0.33 (35914) SS BOND : bond 0.00363 / 0.25 ( 41) SS BOND : angle 1.07662 / 0.80 ( 82) hydrogen bonds : bond 0.04704 / 3.10 ( 977) hydrogen bonds : angle 5.45004 / 3.76 ( 2700) Misc. bond : bond 0.00048 / 0.03 ( 1) link_ALPHA1-4 : bond 0.00325 / 0.17 ( 4) link_ALPHA1-4 : angle 2.32186 / 1.55 ( 12) link_NAG-ASN : bond 0.00346 / 0.18 ( 9) link_NAG-ASN : angle 2.01611 / 1.35 ( 27) *********************** 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 85 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8717 (t80) cc_final: 0.8433 (t80) REVERT: C 869 MET cc_start: 0.9104 (mtt) cc_final: 0.8904 (ptp) REVERT: A 153 MET cc_start: 0.8183 (mpp) cc_final: 0.7901 (mpp) REVERT: B 15 CYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4456 (t) REVERT: B 298 GLU cc_start: 0.9506 (tt0) cc_final: 0.9190 (mt-10) outliers start: 33 outliers final: 19 residues processed: 81 average time/residue: 0.1288 time to fit residues: 18.4182 Evaluate side-chains 70 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL 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 881 THR 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 15 CYS Chi-restraints excluded: chain B residue 33 THR 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 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 861 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 62 optimal weight: 0.0980 chunk 206 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 152 optimal weight: 50.0000 chunk 276 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN C 644 GLN C 709 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.045246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030324 restraints weight = 209521.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031333 restraints weight = 114875.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.031976 restraints weight = 77388.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032445 restraints weight = 59679.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032763 restraints weight = 49835.578| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26438 Z= 0.228 Angle : 0.615 9.829 36035 Z= 0.316 Chirality : 0.043 0.257 4135 Planarity : 0.004 0.054 4619 Dihedral : 7.634 97.470 4002 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.44 % Allowed : 12.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3211 helix: 1.70 (0.20), residues: 686 sheet: -0.32 (0.19), residues: 692 loop : -1.67 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1107 TYR 0.018 0.001 TYR A 873 PHE 0.017 0.001 PHE B 855 TRP 0.014 0.001 TRP C 258 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (26383) covalent geometry : angle 0.61037 / 0.31 (35914) SS BOND : bond 0.00323 / 0.22 ( 41) SS BOND : angle 0.96297 / 0.69 ( 82) hydrogen bonds : bond 0.04598 / 3.04 ( 977) hydrogen bonds : angle 5.37262 / 3.70 ( 2700) Misc. bond : bond 0.00014 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00437 / 0.22 ( 4) link_ALPHA1-4 : angle 2.39459 / 1.60 ( 12) link_NAG-ASN : bond 0.00288 / 0.14 ( 9) link_NAG-ASN : angle 1.99806 / 1.33 ( 27) *********************** 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 92 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 51 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8733 (t80) cc_final: 0.8464 (t80) REVERT: C 317 ASN cc_start: 0.8749 (p0) cc_final: 0.8236 (t0) REVERT: C 869 MET cc_start: 0.9053 (mtt) cc_final: 0.8831 (ptp) REVERT: A 153 MET cc_start: 0.8210 (mpp) cc_final: 0.7907 (mpp) REVERT: B 15 CYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4413 (t) REVERT: B 298 GLU cc_start: 0.9505 (tt0) cc_final: 0.9193 (mt-10) outliers start: 41 outliers final: 26 residues processed: 88 average time/residue: 0.1347 time to fit residues: 21.1612 Evaluate side-chains 75 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 699 LEU 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 598 ILE 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 15 CYS 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 699 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 201 optimal weight: 0.8980 chunk 269 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 152 optimal weight: 50.0000 chunk 239 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 219 optimal weight: 20.0000 chunk 271 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN C 644 GLN A 115 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN B1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.046260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031313 restraints weight = 207474.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.032395 restraints weight = 110799.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033113 restraints weight = 73577.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.033597 restraints weight = 55876.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033928 restraints weight = 46368.136| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26438 Z= 0.113 Angle : 0.533 11.179 36035 Z= 0.274 Chirality : 0.043 0.254 4135 Planarity : 0.004 0.053 4619 Dihedral : 7.077 92.859 4002 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.06 % Allowed : 13.45 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3211 helix: 2.16 (0.21), residues: 672 sheet: -0.17 (0.20), residues: 661 loop : -1.48 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.014 0.001 TYR C1067 PHE 0.014 0.001 PHE B 133 TRP 0.010 0.001 TRP C 152 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (26383) covalent geometry : angle 0.52740 / 0.27 (35914) SS BOND : bond 0.00262 / 0.17 ( 41) SS BOND : angle 0.76553 / 0.56 ( 82) hydrogen bonds : bond 0.04182 / 2.78 ( 977) hydrogen bonds : angle 5.01352 / 3.46 ( 2700) Misc. bond : bond 0.00003 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00308 / 0.16 ( 4) link_ALPHA1-4 : angle 2.59288 / 1.67 ( 12) link_NAG-ASN : bond 0.00230 / 0.11 ( 9) link_NAG-ASN : angle 1.93170 / 1.26 ( 27) *********************** 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 84 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8712 (t80) cc_final: 0.8431 (t80) REVERT: C 644 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: C 869 MET cc_start: 0.9061 (mtt) cc_final: 0.8828 (ptp) REVERT: A 153 MET cc_start: 0.8188 (mpp) cc_final: 0.7865 (mpp) REVERT: B 298 GLU cc_start: 0.9478 (tt0) cc_final: 0.9222 (mt-10) outliers start: 30 outliers final: 21 residues processed: 81 average time/residue: 0.1445 time to fit residues: 20.7585 Evaluate side-chains 71 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 613 GLN Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 881 THR 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 130 VAL Chi-restraints excluded: chain B residue 216 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 231 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 161 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.045989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031112 restraints weight = 209982.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032175 restraints weight = 112647.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.032879 restraints weight = 74729.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033356 restraints weight = 56793.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033649 restraints weight = 47145.308| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26438 Z= 0.166 Angle : 0.557 10.627 36035 Z= 0.285 Chirality : 0.042 0.250 4135 Planarity : 0.004 0.053 4619 Dihedral : 7.015 92.030 4002 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.16 % Allowed : 13.48 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3211 helix: 2.17 (0.21), residues: 673 sheet: -0.17 (0.20), residues: 655 loop : -1.49 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.013 0.001 TYR C1067 PHE 0.013 0.001 PHE B 855 TRP 0.011 0.001 TRP C 258 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (26383) covalent geometry : angle 0.55220 / 0.28 (35914) SS BOND : bond 0.00266 / 0.19 ( 41) SS BOND : angle 0.83898 / 0.59 ( 82) hydrogen bonds : bond 0.04218 / 2.80 ( 977) hydrogen bonds : angle 5.06604 / 3.50 ( 2700) Misc. bond : bond 0.00016 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00371 / 0.19 ( 4) link_ALPHA1-4 : angle 2.59027 / 1.68 ( 12) link_NAG-ASN : bond 0.00206 / 0.10 ( 9) link_NAG-ASN : angle 1.91569 / 1.28 ( 27) *********************** 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 83 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8752 (t80) cc_final: 0.8483 (t80) REVERT: C 317 ASN cc_start: 0.8703 (p0) cc_final: 0.8108 (t0) REVERT: C 869 MET cc_start: 0.9046 (mtt) cc_final: 0.8807 (ptp) REVERT: A 153 MET cc_start: 0.8173 (mpp) cc_final: 0.7845 (mpp) REVERT: B 298 GLU cc_start: 0.9485 (tt0) cc_final: 0.9197 (mt-10) outliers start: 33 outliers final: 26 residues processed: 80 average time/residue: 0.1299 time to fit residues: 18.6895 Evaluate side-chains 74 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 881 THR 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 598 ILE 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 Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 294 optimal weight: 0.1980 chunk 141 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 127 optimal weight: 0.0060 chunk 220 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 overall best weight: 0.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 613 GLN C 616 ASN A 115 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 14 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031885 restraints weight = 204801.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032986 restraints weight = 108602.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033721 restraints weight = 71806.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034226 restraints weight = 54335.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034567 restraints weight = 44831.808| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2559 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= 0.096 Angle : 0.521 10.285 36035 Z= 0.268 Chirality : 0.043 0.246 4135 Planarity : 0.004 0.052 4619 Dihedral : 6.645 88.505 4002 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.81 % Allowed : 13.90 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3211 helix: 2.31 (0.21), residues: 672 sheet: -0.04 (0.20), residues: 659 loop : -1.39 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.014 0.001 TYR C1067 PHE 0.014 0.001 PHE B 133 TRP 0.010 0.001 TRP C 152 HIS 0.002 0.000 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (26383) covalent geometry : angle 0.51586 / 0.27 (35914) SS BOND : bond 0.00248 / 0.15 ( 41) SS BOND : angle 0.84993 / 0.58 ( 82) hydrogen bonds : bond 0.03954 / 2.63 ( 977) hydrogen bonds : angle 4.86121 / 3.38 ( 2700) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00324 / 0.17 ( 4) link_ALPHA1-4 : angle 2.72802 / 1.74 ( 12) link_NAG-ASN : bond 0.00279 / 0.13 ( 9) link_NAG-ASN : angle 1.86310 / 1.22 ( 27) ********************** 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 75 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 ASN cc_start: 0.8630 (p0) cc_final: 0.7913 (t0) REVERT: C 869 MET cc_start: 0.9094 (mtt) cc_final: 0.8821 (ptp) REVERT: A 153 MET cc_start: 0.8167 (mpp) cc_final: 0.7834 (mpp) REVERT: B 298 GLU cc_start: 0.9498 (tt0) cc_final: 0.9233 (mt-10) outliers start: 23 outliers final: 22 residues processed: 72 average time/residue: 0.1375 time to fit residues: 17.3638 Evaluate side-chains 72 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 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 43 optimal weight: 0.0970 chunk 78 optimal weight: 0.0770 chunk 142 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 487 ASN C 616 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 613 GLN ** 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 = 0.3341 r_free = 0.3341 target = 0.046770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031892 restraints weight = 203855.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032995 restraints weight = 108082.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033728 restraints weight = 71474.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034188 restraints weight = 54098.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034549 restraints weight = 45066.082| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 26438 Z= 0.145 Angle : 0.677 59.198 36035 Z= 0.372 Chirality : 0.043 0.351 4135 Planarity : 0.004 0.052 4619 Dihedral : 6.639 88.347 4002 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.84 % Allowed : 13.94 % Favored : 85.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3211 helix: 2.30 (0.21), residues: 672 sheet: -0.03 (0.20), residues: 659 loop : -1.38 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.014 0.001 TYR C1067 PHE 0.013 0.001 PHE B 133 TRP 0.010 0.001 TRP C 152 HIS 0.002 0.000 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (26383) covalent geometry : angle 0.67328 / 0.37 (35914) SS BOND : bond 0.00204 / 0.14 ( 41) SS BOND : angle 0.81369 / 0.56 ( 82) hydrogen bonds : bond 0.03927 / 2.61 ( 977) hydrogen bonds : angle 4.86652 / 3.38 ( 2700) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00346 / 0.18 ( 4) link_ALPHA1-4 : angle 2.76266 / 1.77 ( 12) link_NAG-ASN : bond 0.00278 / 0.13 ( 9) link_NAG-ASN : angle 1.86267 / 1.22 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4024.21 seconds wall clock time: 70 minutes 43.81 seconds (4243.81 seconds total)