Starting phenix.real_space_refine on Fri Mar 6 19:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9q_31036/03_2026/7e9q_31036.cif" } resolution = 3.65 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= 1.000 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 147 5.16 5 C 21504 2.51 5 N 5622 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "Y" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "E" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.52, per 1000 atoms: 0.22 Number of scatterers: 33876 At special positions: 0 Unit cell: (191.625, 205.86, 227.76, 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 147 16.00 O 6603 8.00 N 5622 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 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 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.05 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 65 sheets defined 18.4% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.752A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.584A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.839A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.731A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.587A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.536A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.031A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.933A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.649A 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 984 removed outlier: 3.757A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.074A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.967A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.079A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.540A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.056A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.085A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.159A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.255A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.573A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.641A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.663A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.613A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.617A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.839A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.718A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.556A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.867A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 4.406A pdb=" N GLU L 192 " --> pdb=" O LYS L 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'X' and resid 126 through 132 Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.982A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 4.122A pdb=" N GLU E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASP F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.667A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.415A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.708A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.708A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.614A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB4, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.520A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.952A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB8, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.703A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.296A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.925A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.175A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.834A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.252A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.548A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.944A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.925A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.017A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE9, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.002A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 Processing sheet with id=AF4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'X' and resid 50 through 54 removed outlier: 6.357A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR X 54 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU X 38 " --> pdb=" O TYR X 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 119 through 123 removed outlier: 5.408A pdb=" N SER X 136 " --> pdb=" O LEU X 186 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU X 186 " --> pdb=" O SER X 136 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL X 138 " --> pdb=" O LEU X 184 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU X 184 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU X 140 " --> pdb=" O SER X 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER X 182 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN X 142 " --> pdb=" O LEU X 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU X 180 " --> pdb=" O ASN X 142 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER X 179 " --> pdb=" O GLU X 170 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU X 170 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER X 181 " --> pdb=" O VAL X 168 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL X 168 " --> pdb=" O SER X 181 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR X 183 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU X 166 " --> pdb=" O THR X 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.521A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.758A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 167 through 171 removed outlier: 4.336A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.456A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.710A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.018A pdb=" N LYS E 150 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'F' and resid 45 through 51 removed outlier: 6.445A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 98 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL F 119 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.850A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N CYS F 157 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER F 197 " --> pdb=" O CYS F 157 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 196 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 168 through 170 1314 hydrogen bonds defined for protein. 3495 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: 8.77 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5562 1.30 - 1.43: 9381 1.43 - 1.57: 19509 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.538 1.463 0.075 1.29e-02 6.01e+03 3.36e+01 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.16e-02 7.43e+03 3.30e+01 bond pdb=" C7 NAG A1305 " pdb=" N2 NAG A1305 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C7 NAG C1304 " pdb=" N2 NAG C1304 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C7 NAG A1304 " pdb=" N2 NAG A1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 45404 2.29 - 4.57: 1474 4.57 - 6.86: 235 6.86 - 9.15: 32 9.15 - 11.43: 3 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE X 111 " pdb=" CA ILE X 111 " pdb=" C ILE X 111 " ideal model delta sigma weight residual 110.72 119.54 -8.82 1.01e+00 9.80e-01 7.63e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 121.34 112.69 8.65 1.14e+00 7.69e-01 5.76e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" N PHE A 898 " ideal model delta sigma weight residual 115.56 124.99 -9.43 1.27e+00 6.20e-01 5.51e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.51 -6.71 1.00e+00 1.00e+00 4.50e+01 angle pdb=" N PRO A 897 " pdb=" CA PRO A 897 " pdb=" CB PRO A 897 " ideal model delta sigma weight residual 103.31 97.35 5.96 8.90e-01 1.26e+00 4.48e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 19729 24.08 - 48.16: 961 48.16 - 72.24: 160 72.24 - 96.32: 70 96.32 - 120.40: 107 Dihedral angle restraints: 21027 sinusoidal: 8475 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.80 -84.80 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -1.99 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 176.33 -83.33 1 1.00e+01 1.00e-02 8.48e+01 ... (remaining 21024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4891 0.091 - 0.181: 486 0.181 - 0.272: 40 0.272 - 0.362: 13 0.362 - 0.453: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" CB VAL B 524 " pdb=" CA VAL B 524 " pdb=" CG1 VAL B 524 " pdb=" CG2 VAL B 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA PHE C 338 " pdb=" N PHE C 338 " pdb=" C PHE C 338 " pdb=" CB PHE C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 938 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C LEU B 938 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU B 938 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 939 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C THR B 887 " -0.067 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 84 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU E 84 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU E 84 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3535 2.75 - 3.29: 34221 3.29 - 3.82: 54454 3.82 - 4.36: 63463 4.36 - 4.90: 108003 Nonbonded interactions: 263676 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.209 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.210 3.040 nonbonded pdb=" OG SER X 70 " pdb=" OG1 THR X 77 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.222 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.222 3.040 ... (remaining 263671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'Y' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.580 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.007 0.115 34717 Z= 0.410 Angle : 0.939 11.431 47327 Z= 0.560 Chirality : 0.057 0.453 5433 Planarity : 0.006 0.068 6072 Dihedral : 17.925 120.402 12816 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.27 % Allowed : 1.36 % Favored : 98.38 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.33 % 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: -2.42 (0.12), residues: 4266 helix: 0.11 (0.20), residues: 668 sheet: -1.24 (0.14), residues: 1198 loop : -2.39 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 403 TYR 0.025 0.002 TYR C 674 PHE 0.038 0.002 PHE A 888 TRP 0.045 0.002 TRP Y 36 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00717 (34641) covalent geometry : angle 0.92990 (47148) SS BOND : bond 0.00854 ( 49) SS BOND : angle 2.27835 ( 98) hydrogen bonds : bond 0.13888 ( 1273) hydrogen bonds : angle 7.70122 ( 3495) link_NAG-ASN : bond 0.00434 ( 27) link_NAG-ASN : angle 2.24616 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 323 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7267 (mp) cc_final: 0.6008 (mm) REVERT: C 338 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7716 (t80) REVERT: H 134 LYS cc_start: 0.3646 (ttpp) cc_final: 0.3109 (mttt) REVERT: H 160 LYS cc_start: 0.2854 (mttm) cc_final: 0.1803 (pttm) REVERT: H 212 ILE cc_start: 0.1480 (OUTLIER) cc_final: 0.0726 (mt) REVERT: E 174 LYS cc_start: 0.3081 (mttt) cc_final: 0.2149 (pttt) REVERT: F 43 LYS cc_start: 0.3421 (mmtm) cc_final: 0.2124 (tmtt) outliers start: 10 outliers final: 1 residues processed: 332 average time/residue: 0.2206 time to fit residues: 117.5944 Evaluate side-chains 194 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 40.0000 chunk 155 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN B1005 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 804 GLN C 953 ASN L 142 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.191216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.164957 restraints weight = 67251.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.159360 restraints weight = 88890.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.155294 restraints weight = 81292.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.154381 restraints weight = 79485.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.152899 restraints weight = 59113.156| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34717 Z= 0.140 Angle : 0.700 9.997 47327 Z= 0.350 Chirality : 0.049 0.323 5433 Planarity : 0.005 0.059 6072 Dihedral : 13.963 110.495 5201 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.96 % Allowed : 7.83 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.97 (0.12), residues: 4266 helix: 1.01 (0.20), residues: 659 sheet: -1.01 (0.14), residues: 1199 loop : -2.23 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 24 TYR 0.023 0.001 TYR C1067 PHE 0.024 0.002 PHE X 144 TRP 0.018 0.002 TRP Y 47 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00318 (34641) covalent geometry : angle 0.69028 (47148) SS BOND : bond 0.00437 ( 49) SS BOND : angle 1.68300 ( 98) hydrogen bonds : bond 0.05054 ( 1273) hydrogen bonds : angle 6.33509 ( 3495) link_NAG-ASN : bond 0.00389 ( 27) link_NAG-ASN : angle 2.42502 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1107 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (mtt-85) REVERT: A 358 ILE cc_start: 0.7310 (mp) cc_final: 0.6821 (mm) REVERT: A 697 MET cc_start: 0.7415 (mtp) cc_final: 0.6999 (ttm) REVERT: A 902 MET cc_start: 0.8696 (tpt) cc_final: 0.8481 (tpt) REVERT: H 84 ARG cc_start: 0.4223 (ptt90) cc_final: 0.3702 (ptt90) REVERT: H 102 MET cc_start: 0.4717 (pmm) cc_final: 0.4456 (pmm) REVERT: H 134 LYS cc_start: 0.3427 (ttpp) cc_final: 0.3092 (mttt) REVERT: H 160 LYS cc_start: 0.2894 (mttm) cc_final: 0.1671 (pttm) REVERT: X 53 ILE cc_start: 0.5883 (mm) cc_final: 0.5682 (mp) REVERT: F 43 LYS cc_start: 0.3388 (mmtm) cc_final: 0.2144 (tmtt) outliers start: 36 outliers final: 21 residues processed: 250 average time/residue: 0.2074 time to fit residues: 84.7160 Evaluate side-chains 198 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 17 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 415 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 564 GLN C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.190053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.163891 restraints weight = 66073.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.156811 restraints weight = 90901.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151968 restraints weight = 99640.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.152172 restraints weight = 93097.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.151469 restraints weight = 65635.074| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34717 Z= 0.127 Angle : 0.649 10.374 47327 Z= 0.323 Chirality : 0.047 0.325 5433 Planarity : 0.005 0.058 6072 Dihedral : 10.365 106.319 5198 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.30 % Allowed : 11.00 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.73 (0.13), residues: 4266 helix: 1.29 (0.20), residues: 666 sheet: -0.85 (0.14), residues: 1230 loop : -2.11 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 16 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE H 163 TRP 0.019 0.001 TRP Y 47 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00287 (34641) covalent geometry : angle 0.63901 (47148) SS BOND : bond 0.00335 ( 49) SS BOND : angle 1.55492 ( 98) hydrogen bonds : bond 0.04533 ( 1273) hydrogen bonds : angle 5.96482 ( 3495) link_NAG-ASN : bond 0.00393 ( 27) link_NAG-ASN : angle 2.28721 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASN cc_start: 0.6442 (m-40) cc_final: 0.6010 (t0) REVERT: A 697 MET cc_start: 0.7374 (mtp) cc_final: 0.7073 (ttm) REVERT: C 954 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: H 102 MET cc_start: 0.4433 (pmm) cc_final: 0.4096 (pmm) REVERT: H 134 LYS cc_start: 0.3326 (ttpp) cc_final: 0.2727 (ptpt) REVERT: H 160 LYS cc_start: 0.2700 (mttm) cc_final: 0.1680 (pttm) REVERT: Y 32 TYR cc_start: 0.7860 (m-80) cc_final: 0.7584 (m-80) REVERT: E 35 TYR cc_start: 0.1509 (OUTLIER) cc_final: 0.0900 (t80) REVERT: F 43 LYS cc_start: 0.3408 (mmtm) cc_final: 0.2184 (tmtt) outliers start: 49 outliers final: 30 residues processed: 257 average time/residue: 0.1996 time to fit residues: 84.5046 Evaluate side-chains 220 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 111 ILE Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 161 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN C 928 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS X 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.192398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.164479 restraints weight = 66558.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.159262 restraints weight = 101642.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.156114 restraints weight = 82642.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154759 restraints weight = 80671.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.154021 restraints weight = 62975.040| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34717 Z= 0.130 Angle : 0.627 11.081 47327 Z= 0.313 Chirality : 0.046 0.239 5433 Planarity : 0.004 0.061 6072 Dihedral : 8.567 101.838 5198 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.32 % Allowed : 12.22 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.61 (0.13), residues: 4266 helix: 1.35 (0.20), residues: 664 sheet: -0.72 (0.14), residues: 1205 loop : -2.04 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.020 0.001 TYR C1067 PHE 0.033 0.001 PHE B 135 TRP 0.019 0.001 TRP Y 47 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (34641) covalent geometry : angle 0.61597 (47148) SS BOND : bond 0.00354 ( 49) SS BOND : angle 1.61649 ( 98) hydrogen bonds : bond 0.04472 ( 1273) hydrogen bonds : angle 5.79380 ( 3495) link_NAG-ASN : bond 0.00324 ( 27) link_NAG-ASN : angle 2.44504 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5101 (p0) cc_final: 0.4772 (p0) REVERT: B 343 ASN cc_start: 0.6392 (m-40) cc_final: 0.5893 (t0) REVERT: B 660 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: B 977 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 697 MET cc_start: 0.7356 (mtp) cc_final: 0.7138 (ttm) REVERT: H 102 MET cc_start: 0.4481 (pmm) cc_final: 0.3937 (pmm) REVERT: H 134 LYS cc_start: 0.2974 (ttpp) cc_final: 0.2488 (ptpt) REVERT: H 160 LYS cc_start: 0.2656 (mttm) cc_final: 0.1719 (pttp) REVERT: X 147 ARG cc_start: 0.6308 (tpt90) cc_final: 0.5727 (mmm160) REVERT: Y 101 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4495 (mp0) REVERT: E 35 TYR cc_start: 0.1693 (OUTLIER) cc_final: 0.1072 (t80) REVERT: E 174 LYS cc_start: 0.3162 (mttt) cc_final: 0.2204 (pttt) REVERT: F 43 LYS cc_start: 0.3494 (mmtm) cc_final: 0.2301 (tmtt) REVERT: F 214 ASN cc_start: 0.2236 (OUTLIER) cc_final: 0.1653 (t0) outliers start: 87 outliers final: 49 residues processed: 296 average time/residue: 0.2034 time to fit residues: 100.4522 Evaluate side-chains 249 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 1 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 383 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.189363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.161362 restraints weight = 66963.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.156636 restraints weight = 101650.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.153399 restraints weight = 85386.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153473 restraints weight = 78288.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.152058 restraints weight = 59058.553| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34717 Z= 0.174 Angle : 0.658 11.152 47327 Z= 0.331 Chirality : 0.047 0.244 5433 Planarity : 0.005 0.062 6072 Dihedral : 8.098 96.507 5198 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.53 % Allowed : 13.55 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.66 (0.13), residues: 4266 helix: 1.18 (0.20), residues: 658 sheet: -0.74 (0.14), residues: 1220 loop : -2.03 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 905 TYR 0.050 0.002 TYR L 145 PHE 0.041 0.002 PHE B 135 TRP 0.023 0.001 TRP L 40 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00416 (34641) covalent geometry : angle 0.64568 (47148) SS BOND : bond 0.00454 ( 49) SS BOND : angle 1.72661 ( 98) hydrogen bonds : bond 0.04892 ( 1273) hydrogen bonds : angle 5.84665 ( 3495) link_NAG-ASN : bond 0.00296 ( 27) link_NAG-ASN : angle 2.62781 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 202 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5261 (p0) cc_final: 0.4907 (p0) REVERT: B 343 ASN cc_start: 0.6390 (m-40) cc_final: 0.5930 (t0) REVERT: B 660 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: B 977 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7663 (pp) REVERT: A 697 MET cc_start: 0.7431 (mtp) cc_final: 0.7215 (ttm) REVERT: C 950 ASP cc_start: 0.7121 (p0) cc_final: 0.6881 (p0) REVERT: C 1063 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (pp) REVERT: C 1107 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7310 (mtt90) REVERT: H 134 LYS cc_start: 0.3032 (ttpp) cc_final: 0.2373 (ptpt) REVERT: H 160 LYS cc_start: 0.2615 (mttm) cc_final: 0.1633 (pttm) REVERT: Y 101 GLU cc_start: 0.5304 (OUTLIER) cc_final: 0.4420 (mp0) REVERT: E 35 TYR cc_start: 0.1944 (OUTLIER) cc_final: 0.1219 (t80) REVERT: E 174 LYS cc_start: 0.3229 (mttt) cc_final: 0.2249 (pttt) REVERT: F 43 LYS cc_start: 0.3383 (mmtm) cc_final: 0.2152 (tmtt) REVERT: F 214 ASN cc_start: 0.2248 (OUTLIER) cc_final: 0.1731 (t0) outliers start: 95 outliers final: 63 residues processed: 285 average time/residue: 0.2062 time to fit residues: 96.7261 Evaluate side-chains 262 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 76 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 281 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN L 6 GLN ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.191580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.164954 restraints weight = 66790.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.160195 restraints weight = 91232.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.155645 restraints weight = 76399.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153658 restraints weight = 77515.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.153050 restraints weight = 60174.575| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34717 Z= 0.115 Angle : 0.606 10.638 47327 Z= 0.303 Chirality : 0.045 0.241 5433 Planarity : 0.004 0.061 6072 Dihedral : 7.423 90.356 5198 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.08 % Allowed : 14.67 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.47 (0.13), residues: 4266 helix: 1.42 (0.20), residues: 665 sheet: -0.64 (0.15), residues: 1205 loop : -1.93 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 214 TYR 0.026 0.001 TYR L 145 PHE 0.039 0.001 PHE B 135 TRP 0.022 0.001 TRP L 40 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (34641) covalent geometry : angle 0.59375 (47148) SS BOND : bond 0.00317 ( 49) SS BOND : angle 1.57795 ( 98) hydrogen bonds : bond 0.04249 ( 1273) hydrogen bonds : angle 5.58520 ( 3495) link_NAG-ASN : bond 0.00305 ( 27) link_NAG-ASN : angle 2.56374 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5255 (p0) cc_final: 0.4973 (p0) REVERT: B 343 ASN cc_start: 0.6354 (m-40) cc_final: 0.5849 (t0) REVERT: B 977 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7621 (pp) REVERT: A 212 LEU cc_start: 0.4547 (mt) cc_final: 0.4317 (tt) REVERT: A 392 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: C 1107 ARG cc_start: 0.7642 (ttm170) cc_final: 0.7343 (mtt90) REVERT: H 102 MET cc_start: 0.4456 (pmm) cc_final: 0.4094 (pmm) REVERT: H 160 LYS cc_start: 0.2476 (mttm) cc_final: 0.1659 (pttm) REVERT: X 54 TYR cc_start: 0.5064 (t80) cc_final: 0.4428 (t80) REVERT: Y 101 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4309 (mp0) REVERT: E 35 TYR cc_start: 0.1880 (OUTLIER) cc_final: 0.1165 (t80) REVERT: F 43 LYS cc_start: 0.3324 (mmtm) cc_final: 0.2275 (tmtt) REVERT: F 214 ASN cc_start: 0.2055 (OUTLIER) cc_final: 0.1587 (t0) outliers start: 78 outliers final: 57 residues processed: 281 average time/residue: 0.2009 time to fit residues: 93.7161 Evaluate side-chains 250 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 240 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 380 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.185238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.157471 restraints weight = 66473.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.151957 restraints weight = 99435.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.149510 restraints weight = 78770.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.148949 restraints weight = 77440.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.147424 restraints weight = 66056.825| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 34717 Z= 0.204 Angle : 0.675 11.008 47327 Z= 0.340 Chirality : 0.047 0.244 5433 Planarity : 0.005 0.061 6072 Dihedral : 7.296 88.283 5198 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.53 % Allowed : 15.36 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.61 (0.13), residues: 4266 helix: 1.06 (0.20), residues: 663 sheet: -0.67 (0.14), residues: 1212 loop : -1.98 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 59 TYR 0.024 0.002 TYR B 170 PHE 0.039 0.002 PHE B 135 TRP 0.018 0.001 TRP L 40 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00499 (34641) covalent geometry : angle 0.66142 (47148) SS BOND : bond 0.00386 ( 49) SS BOND : angle 1.65533 ( 98) hydrogen bonds : bond 0.05153 ( 1273) hydrogen bonds : angle 5.77360 ( 3495) link_NAG-ASN : bond 0.00325 ( 27) link_NAG-ASN : angle 2.84192 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 182 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5248 (p0) cc_final: 0.4946 (p0) REVERT: B 343 ASN cc_start: 0.6282 (m-40) cc_final: 0.5788 (t0) REVERT: B 660 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 722 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8876 (m) REVERT: B 977 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7686 (pp) REVERT: A 212 LEU cc_start: 0.4454 (mt) cc_final: 0.4253 (tt) REVERT: A 392 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: C 900 MET cc_start: 0.7772 (mtp) cc_final: 0.7373 (mtp) REVERT: C 1107 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7407 (mtt90) REVERT: H 83 MET cc_start: 0.2365 (OUTLIER) cc_final: 0.1518 (ptp) REVERT: H 160 LYS cc_start: 0.3050 (mttm) cc_final: 0.2049 (pttm) REVERT: Y 101 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4354 (mp0) REVERT: E 4 MET cc_start: 0.2715 (tpp) cc_final: 0.2407 (tpp) REVERT: E 35 TYR cc_start: 0.2242 (OUTLIER) cc_final: 0.1463 (t80) REVERT: F 43 LYS cc_start: 0.3454 (mmtm) cc_final: 0.2149 (tmtt) REVERT: F 214 ASN cc_start: 0.2066 (OUTLIER) cc_final: 0.1544 (t0) outliers start: 95 outliers final: 69 residues processed: 270 average time/residue: 0.1976 time to fit residues: 89.3399 Evaluate side-chains 253 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 307 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 347 optimal weight: 8.9990 chunk 288 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.186419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.158507 restraints weight = 66223.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.153663 restraints weight = 100654.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149279 restraints weight = 82861.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.147619 restraints weight = 81579.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.146187 restraints weight = 61935.283| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34717 Z= 0.140 Angle : 0.626 10.588 47327 Z= 0.314 Chirality : 0.045 0.242 5433 Planarity : 0.005 0.062 6072 Dihedral : 6.947 86.126 5198 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.37 % Allowed : 15.84 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.50 (0.13), residues: 4266 helix: 1.25 (0.20), residues: 663 sheet: -0.58 (0.15), residues: 1212 loop : -1.96 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 214 TYR 0.021 0.001 TYR C1067 PHE 0.035 0.001 PHE B 135 TRP 0.018 0.001 TRP L 40 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00330 (34641) covalent geometry : angle 0.61337 (47148) SS BOND : bond 0.00349 ( 49) SS BOND : angle 1.52803 ( 98) hydrogen bonds : bond 0.04657 ( 1273) hydrogen bonds : angle 5.62112 ( 3495) link_NAG-ASN : bond 0.00273 ( 27) link_NAG-ASN : angle 2.68825 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 192 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5296 (p0) cc_final: 0.5093 (p0) REVERT: B 343 ASN cc_start: 0.6548 (m-40) cc_final: 0.5967 (t0) REVERT: B 722 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8873 (m) REVERT: B 977 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7646 (pp) REVERT: A 212 LEU cc_start: 0.4662 (mt) cc_final: 0.4376 (tt) REVERT: A 392 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: C 900 MET cc_start: 0.8405 (mtp) cc_final: 0.8040 (mtp) REVERT: C 950 ASP cc_start: 0.7012 (p0) cc_final: 0.6783 (p0) REVERT: C 1063 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8120 (pp) REVERT: H 83 MET cc_start: 0.2248 (OUTLIER) cc_final: 0.1415 (ptp) REVERT: H 160 LYS cc_start: 0.2810 (mttm) cc_final: 0.1901 (pttm) REVERT: X 54 TYR cc_start: 0.5163 (t80) cc_final: 0.4856 (t80) REVERT: Y 101 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4421 (mp0) REVERT: Y 117 MET cc_start: 0.4826 (mmt) cc_final: 0.4594 (mmm) REVERT: E 4 MET cc_start: 0.2588 (tpp) cc_final: 0.2268 (tpp) REVERT: E 35 TYR cc_start: 0.2076 (OUTLIER) cc_final: 0.1345 (t80) REVERT: F 43 LYS cc_start: 0.3572 (mmtm) cc_final: 0.2337 (tmtt) REVERT: F 214 ASN cc_start: 0.1999 (OUTLIER) cc_final: 0.1460 (t0) outliers start: 89 outliers final: 67 residues processed: 274 average time/residue: 0.1955 time to fit residues: 90.5198 Evaluate side-chains 256 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 141 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 403 optimal weight: 20.0000 chunk 340 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 391 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 309 optimal weight: 8.9990 chunk 414 optimal weight: 30.0000 chunk 395 optimal weight: 20.0000 chunk 276 optimal weight: 0.0870 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 953 ASN ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS ** F 39 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 = 0.4582 r_free = 0.4582 target = 0.183215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153796 restraints weight = 65347.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.146606 restraints weight = 110249.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.142562 restraints weight = 100861.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.143108 restraints weight = 91681.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.142949 restraints weight = 60782.770| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 34717 Z= 0.216 Angle : 0.689 11.401 47327 Z= 0.349 Chirality : 0.048 0.260 5433 Planarity : 0.005 0.071 6072 Dihedral : 6.974 83.997 5198 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.64 (0.13), residues: 4266 helix: 0.95 (0.20), residues: 663 sheet: -0.62 (0.15), residues: 1212 loop : -2.01 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 214 TYR 0.025 0.002 TYR B 170 PHE 0.035 0.002 PHE B 135 TRP 0.024 0.002 TRP L 40 HIS 0.004 0.001 HIS X 31 Details of bonding type rmsd covalent geometry : bond 0.00531 (34641) covalent geometry : angle 0.67445 (47148) SS BOND : bond 0.00395 ( 49) SS BOND : angle 1.85184 ( 98) hydrogen bonds : bond 0.05354 ( 1273) hydrogen bonds : angle 5.81855 ( 3495) link_NAG-ASN : bond 0.00325 ( 27) link_NAG-ASN : angle 2.87444 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 183 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASN cc_start: 0.6553 (m-40) cc_final: 0.5943 (t0) REVERT: B 660 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 722 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8869 (m) REVERT: B 977 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7670 (pp) REVERT: A 392 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: C 497 PHE cc_start: 0.5005 (OUTLIER) cc_final: 0.4529 (m-10) REVERT: C 900 MET cc_start: 0.7885 (mtp) cc_final: 0.7501 (mtp) REVERT: C 950 ASP cc_start: 0.6837 (p0) cc_final: 0.6539 (p0) REVERT: H 83 MET cc_start: 0.2234 (OUTLIER) cc_final: 0.1405 (ptp) REVERT: H 98 LYS cc_start: 0.4954 (tptm) cc_final: 0.4699 (tptm) REVERT: H 160 LYS cc_start: 0.2809 (mttm) cc_final: 0.1811 (pttm) REVERT: Y 101 GLU cc_start: 0.5340 (OUTLIER) cc_final: 0.4333 (mp0) REVERT: Y 120 TRP cc_start: 0.5559 (OUTLIER) cc_final: 0.5184 (m-90) REVERT: E 4 MET cc_start: 0.2530 (tpp) cc_final: 0.2142 (tpp) REVERT: E 35 TYR cc_start: 0.2465 (OUTLIER) cc_final: 0.1664 (t80) REVERT: E 174 LYS cc_start: 0.2804 (mttt) cc_final: 0.2121 (pttt) REVERT: F 43 LYS cc_start: 0.3639 (mmtm) cc_final: 0.2355 (tmtt) REVERT: F 69 THR cc_start: -0.0016 (OUTLIER) cc_final: -0.0259 (m) REVERT: F 214 ASN cc_start: 0.2069 (OUTLIER) cc_final: 0.1503 (t0) outliers start: 93 outliers final: 74 residues processed: 266 average time/residue: 0.1958 time to fit residues: 87.4605 Evaluate side-chains 254 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 169 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 74 optimal weight: 0.1980 chunk 355 optimal weight: 6.9990 chunk 309 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 409 optimal weight: 20.0000 chunk 224 optimal weight: 0.0030 chunk 244 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 384 optimal weight: 7.9990 overall best weight: 4.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS E 95 GLN ** F 39 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 = 0.4572 r_free = 0.4572 target = 0.182668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.154093 restraints weight = 66044.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148429 restraints weight = 101506.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.145699 restraints weight = 82897.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.144511 restraints weight = 83876.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.142676 restraints weight = 69812.938| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 34717 Z= 0.262 Angle : 0.736 12.164 47327 Z= 0.374 Chirality : 0.049 0.283 5433 Planarity : 0.005 0.058 6072 Dihedral : 7.080 81.261 5198 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.45 % Allowed : 16.21 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.80 (0.12), residues: 4266 helix: 0.70 (0.20), residues: 663 sheet: -0.71 (0.14), residues: 1215 loop : -2.09 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 214 TYR 0.031 0.002 TYR B 170 PHE 0.035 0.002 PHE B 135 TRP 0.020 0.002 TRP L 40 HIS 0.005 0.001 HIS X 31 Details of bonding type rmsd covalent geometry : bond 0.00645 (34641) covalent geometry : angle 0.72100 (47148) SS BOND : bond 0.00436 ( 49) SS BOND : angle 1.99671 ( 98) hydrogen bonds : bond 0.05835 ( 1273) hydrogen bonds : angle 5.99449 ( 3495) link_NAG-ASN : bond 0.00378 ( 27) link_NAG-ASN : angle 3.01619 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 172 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ARG cc_start: 0.6438 (tpm170) cc_final: 0.6145 (tpp-160) REVERT: B 343 ASN cc_start: 0.6534 (m-40) cc_final: 0.5987 (t0) REVERT: B 660 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: B 722 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.8984 (m) REVERT: B 977 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7756 (pp) REVERT: A 392 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: C 497 PHE cc_start: 0.4946 (OUTLIER) cc_final: 0.4576 (m-10) REVERT: C 900 MET cc_start: 0.7910 (mtp) cc_final: 0.7517 (mtp) REVERT: C 1063 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8479 (pp) REVERT: H 83 MET cc_start: 0.2354 (OUTLIER) cc_final: 0.1533 (ptp) REVERT: H 160 LYS cc_start: 0.3075 (mttm) cc_final: 0.1963 (pttm) REVERT: Y 101 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.4573 (mp0) REVERT: Y 120 TRP cc_start: 0.5473 (OUTLIER) cc_final: 0.5126 (m-90) REVERT: E 4 MET cc_start: 0.2670 (tpp) cc_final: 0.2281 (tpp) REVERT: E 35 TYR cc_start: 0.2623 (OUTLIER) cc_final: 0.1851 (t80) REVERT: E 195 LYS cc_start: 0.4195 (mmtt) cc_final: 0.3190 (tmmt) REVERT: F 43 LYS cc_start: 0.3661 (mmtm) cc_final: 0.2240 (tmtt) REVERT: F 214 ASN cc_start: 0.2389 (OUTLIER) cc_final: 0.1701 (t0) outliers start: 92 outliers final: 76 residues processed: 257 average time/residue: 0.1923 time to fit residues: 83.0195 Evaluate side-chains 254 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 120 TRP Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 198 VAL Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 121 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 422 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS E 95 GLN ** F 39 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 = 0.4600 r_free = 0.4600 target = 0.185233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.158453 restraints weight = 65951.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.152834 restraints weight = 95813.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148639 restraints weight = 81151.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.146362 restraints weight = 81426.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.145475 restraints weight = 65950.575| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34717 Z= 0.154 Angle : 0.651 10.996 47327 Z= 0.328 Chirality : 0.046 0.246 5433 Planarity : 0.005 0.060 6072 Dihedral : 6.715 79.591 5198 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.42 % Allowed : 16.37 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.61 (0.13), residues: 4266 helix: 1.05 (0.20), residues: 669 sheet: -0.65 (0.15), residues: 1215 loop : -2.01 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 214 TYR 0.023 0.001 TYR C1067 PHE 0.033 0.002 PHE B 135 TRP 0.015 0.001 TRP Y 47 HIS 0.007 0.001 HIS X 31 Details of bonding type rmsd covalent geometry : bond 0.00366 (34641) covalent geometry : angle 0.63685 (47148) SS BOND : bond 0.00350 ( 49) SS BOND : angle 1.75774 ( 98) hydrogen bonds : bond 0.04943 ( 1273) hydrogen bonds : angle 5.73419 ( 3495) link_NAG-ASN : bond 0.00277 ( 27) link_NAG-ASN : angle 2.73614 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.55 seconds wall clock time: 92 minutes 56.56 seconds (5576.56 seconds total)