Starting phenix.real_space_refine on Mon Jul 6 07:29:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9q_31036/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_2026/7e9q_31036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9q_31036/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 9 Time building chain proxies: 6.99, per 1000 atoms: 0.21 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 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: 1.17 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: 10.60 Time building geometry restraints manager: 3.91 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 - 17.99: 18623 17.99 - 35.98: 1512 35.98 - 53.97: 247 53.97 - 71.96: 45 71.96 - 89.95: 33 Dihedral angle restraints: 20460 sinusoidal: 7908 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 20457 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: 0.04 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: 3.660 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: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 34.570 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.160 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 13.467 89.953 12249 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/Z covalent geometry : bond 0.00717 / 0.41 (34641) covalent geometry : angle 0.92990 / 0.56 (47148) SS BOND : bond 0.00854 / 0.57 ( 49) SS BOND : angle 2.27835 / 1.57 ( 98) hydrogen bonds : bond 0.13888 / 8.64 ( 1273) hydrogen bonds : angle 7.70122 / 5.28 ( 3495) link_NAG-ASN : bond 0.00434 / 0.30 ( 27) link_NAG-ASN : angle 2.24616 / 1.64 ( 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 : 1.227 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: 0.2057 time to fit residues: 109.9885 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 : 1.173 ------------------------------------------------------------------------------- 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... B 935 GLN B1005 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.189803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.163574 restraints weight = 66477.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.157238 restraints weight = 92959.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.154670 restraints weight = 85805.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.153933 restraints weight = 74962.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150830 restraints weight = 66885.189| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34717 Z= 0.141 Angle : 0.675 10.767 47327 Z= 0.345 Chirality : 0.049 0.532 5433 Planarity : 0.005 0.061 6072 Dihedral : 5.435 53.759 4634 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.99 % Allowed : 7.80 % 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: -1.98 (0.12), residues: 4266 helix: 1.00 (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 0.007 0.001 ARG X 24 TYR 0.022 0.001 TYR C1067 PHE 0.027 0.002 PHE X 144 TRP 0.017 0.002 TRP Y 47 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (34641) covalent geometry : angle 0.66642 / 0.34 (47148) SS BOND : bond 0.00599 / 0.45 ( 49) SS BOND : angle 1.65832 / 1.24 ( 98) hydrogen bonds : bond 0.05110 / 3.37 ( 1273) hydrogen bonds : angle 6.35848 / 4.37 ( 3495) link_NAG-ASN : bond 0.00430 / 0.29 ( 27) link_NAG-ASN : angle 2.09470 / 1.50 ( 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 263 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.105 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: A 697 MET cc_start: 0.7432 (mtp) cc_final: 0.6980 (ttm) REVERT: H 84 ARG cc_start: 0.4202 (ptt90) cc_final: 0.3717 (ptt90) REVERT: H 102 MET cc_start: 0.4705 (pmm) cc_final: 0.4448 (pmm) REVERT: H 134 LYS cc_start: 0.3430 (ttpp) cc_final: 0.3059 (mttt) REVERT: H 160 LYS cc_start: 0.2939 (mttm) cc_final: 0.1707 (pttm) REVERT: X 53 ILE cc_start: 0.5897 (mm) cc_final: 0.5686 (mp) REVERT: F 43 LYS cc_start: 0.3373 (mmtm) cc_final: 0.2114 (tmtt) outliers start: 37 outliers final: 21 residues processed: 252 average time/residue: 0.1878 time to fit residues: 76.9331 Evaluate side-chains 197 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 380 optimal weight: 7.9990 chunk 415 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 253 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 564 GLN C 218 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.190128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.163924 restraints weight = 65924.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.158128 restraints weight = 90681.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.153679 restraints weight = 84017.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.152582 restraints weight = 82191.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.151646 restraints weight = 63202.807| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34717 Z= 0.129 Angle : 0.624 11.108 47327 Z= 0.318 Chirality : 0.048 0.475 5433 Planarity : 0.005 0.058 6072 Dihedral : 5.114 53.972 4631 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.46 % Allowed : 11.02 % Favored : 87.51 % 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: -1.74 (0.13), residues: 4266 helix: 1.27 (0.20), residues: 665 sheet: -0.85 (0.14), residues: 1229 loop : -2.12 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 16 TYR 0.020 0.001 TYR C1067 PHE 0.027 0.001 PHE B 135 TRP 0.020 0.001 TRP Y 47 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (34641) covalent geometry : angle 0.61643 / 0.32 (47148) SS BOND : bond 0.00345 / 0.23 ( 49) SS BOND : angle 1.50729 / 1.08 ( 98) hydrogen bonds : bond 0.04589 / 3.04 ( 1273) hydrogen bonds : angle 5.98999 / 4.11 ( 3495) link_NAG-ASN : bond 0.00402 / 0.27 ( 27) link_NAG-ASN : angle 1.86965 / 1.33 ( 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 268 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.141 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: 0.6421 (m-40) cc_final: 0.5998 (t0) REVERT: B 660 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: A 697 MET cc_start: 0.7378 (mtp) cc_final: 0.7077 (ttm) REVERT: C 954 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: H 102 MET cc_start: 0.4441 (pmm) cc_final: 0.4100 (pmm) REVERT: H 126 VAL cc_start: 0.5198 (t) cc_final: 0.4978 (p) REVERT: H 134 LYS cc_start: 0.3399 (ttpp) cc_final: 0.2927 (mttt) REVERT: H 160 LYS cc_start: 0.2575 (mttm) cc_final: 0.1561 (pttm) REVERT: E 4 MET cc_start: 0.2832 (tpp) cc_final: 0.2591 (tpp) REVERT: E 35 TYR cc_start: 0.1538 (OUTLIER) cc_final: 0.0918 (t80) REVERT: F 43 LYS cc_start: 0.3418 (mmtm) cc_final: 0.2180 (tmtt) outliers start: 55 outliers final: 35 residues processed: 256 average time/residue: 0.2101 time to fit residues: 90.3217 Evaluate side-chains 225 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 660 TYR 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 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 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 912 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain L residue 138 VAL 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 E residue 196 VAL 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: 0.9990 chunk 253 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 291 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4646 r_free = 0.4646 target = 0.192935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.164997 restraints weight = 66539.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.158395 restraints weight = 91607.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153165 restraints weight = 98026.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.153523 restraints weight = 87873.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.152928 restraints weight = 62975.105| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34717 Z= 0.128 Angle : 0.607 11.354 47327 Z= 0.308 Chirality : 0.047 0.436 5433 Planarity : 0.004 0.061 6072 Dihedral : 4.960 54.715 4631 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.32 % Allowed : 12.25 % Favored : 85.44 % 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: -1.62 (0.13), residues: 4266 helix: 1.33 (0.20), residues: 664 sheet: -0.72 (0.14), residues: 1211 loop : -2.06 (0.12), residues: 2391 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 0.018 0.001 TRP Y 47 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (34641) covalent geometry : angle 0.59895 / 0.31 (47148) SS BOND : bond 0.00375 / 0.26 ( 49) SS BOND : angle 1.57183 / 1.10 ( 98) hydrogen bonds : bond 0.04477 / 2.97 ( 1273) hydrogen bonds : angle 5.81624 / 3.99 ( 3495) link_NAG-ASN : bond 0.00344 / 0.23 ( 27) link_NAG-ASN : angle 1.79919 / 1.27 ( 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 305 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 218 time to evaluate : 1.323 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 111 ASP cc_start: 0.5209 (p0) cc_final: 0.4859 (p0) REVERT: B 343 ASN cc_start: 0.6517 (m-40) cc_final: 0.5979 (t0) REVERT: B 660 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 977 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 697 MET cc_start: 0.7329 (mtp) cc_final: 0.7095 (ttm) REVERT: H 102 MET cc_start: 0.4493 (pmm) cc_final: 0.3960 (pmm) REVERT: H 134 LYS cc_start: 0.3058 (ttpp) cc_final: 0.2483 (ptpt) REVERT: H 160 LYS cc_start: 0.2635 (mttm) cc_final: 0.1687 (pttp) REVERT: Y 101 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4414 (mp0) REVERT: E 35 TYR cc_start: 0.1667 (OUTLIER) cc_final: 0.1054 (t80) REVERT: E 174 LYS cc_start: 0.3156 (mttt) cc_final: 0.2231 (pttt) REVERT: F 43 LYS cc_start: 0.3468 (mmtm) cc_final: 0.2276 (tmtt) REVERT: F 214 ASN cc_start: 0.2254 (OUTLIER) cc_final: 0.1656 (t0) outliers start: 87 outliers final: 46 residues processed: 290 average time/residue: 0.2112 time to fit residues: 102.6001 Evaluate side-chains 240 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 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 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 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 196 VAL Chi-restraints excluded: chain E residue 215 ASN 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: 2.9990 chunk 315 optimal weight: 20.0000 chunk 169 optimal weight: 0.4980 chunk 350 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 137 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 383 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 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 = 0.4646 r_free = 0.4646 target = 0.191559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.163301 restraints weight = 67234.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.157999 restraints weight = 106883.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.155097 restraints weight = 95115.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.155593 restraints weight = 79456.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.154828 restraints weight = 57694.583| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34717 Z= 0.118 Angle : 0.598 11.524 47327 Z= 0.302 Chirality : 0.047 0.407 5433 Planarity : 0.004 0.059 6072 Dihedral : 4.823 54.775 4631 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.34 % Allowed : 13.23 % Favored : 84.42 % 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: -1.51 (0.13), residues: 4266 helix: 1.41 (0.21), residues: 665 sheet: -0.67 (0.14), residues: 1214 loop : -1.97 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.052 0.001 TYR L 145 PHE 0.041 0.001 PHE B 135 TRP 0.025 0.001 TRP L 40 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (34641) covalent geometry : angle 0.58996 / 0.30 (47148) SS BOND : bond 0.00336 / 0.23 ( 49) SS BOND : angle 1.60075 / 1.14 ( 98) hydrogen bonds : bond 0.04259 / 2.82 ( 1273) hydrogen bonds : angle 5.68000 / 3.91 ( 3495) link_NAG-ASN : bond 0.00342 / 0.23 ( 27) link_NAG-ASN : angle 1.71904 / 1.21 ( 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 293 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 1.362 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: 0.5157 (p0) cc_final: 0.4890 (p0) REVERT: B 343 ASN cc_start: 0.6332 (m-40) cc_final: 0.5895 (t0) REVERT: B 977 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7583 (pp) REVERT: A 212 LEU cc_start: 0.4503 (mt) cc_final: 0.4223 (tt) REVERT: C 950 ASP cc_start: 0.6914 (p0) cc_final: 0.6589 (p0) REVERT: C 983 ARG cc_start: 0.6927 (mtm180) cc_final: 0.6703 (ptt180) REVERT: L 65 ASP cc_start: 0.6254 (m-30) cc_final: 0.5960 (m-30) REVERT: H 72 ARG cc_start: 0.5695 (ttt180) cc_final: 0.5419 (ttt90) REVERT: H 134 LYS cc_start: 0.3102 (ttpp) cc_final: 0.2410 (ptpt) REVERT: H 160 LYS cc_start: 0.2514 (mttm) cc_final: 0.1643 (pttm) REVERT: Y 101 GLU cc_start: 0.5210 (OUTLIER) cc_final: 0.4214 (mp0) REVERT: E 35 TYR cc_start: 0.1765 (OUTLIER) cc_final: 0.1090 (t80) REVERT: E 174 LYS cc_start: 0.3186 (mttt) cc_final: 0.2211 (pttt) REVERT: F 43 LYS cc_start: 0.3347 (mmtm) cc_final: 0.2146 (tmtt) REVERT: F 214 ASN cc_start: 0.2126 (OUTLIER) cc_final: 0.1640 (t0) outliers start: 88 outliers final: 57 residues processed: 280 average time/residue: 0.2173 time to fit residues: 101.1532 Evaluate side-chains 256 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 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 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 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 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 568 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 1029 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain L residue 75 ASP 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 83 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 E residue 215 ASN Chi-restraints excluded: chain F residue 65 LYS 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: 2.9990 chunk 275 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 281 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 70 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.193886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.167894 restraints weight = 67053.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.162253 restraints weight = 87226.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157263 restraints weight = 81788.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155510 restraints weight = 79743.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154280 restraints weight = 65924.119| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34717 Z= 0.115 Angle : 0.586 11.409 47327 Z= 0.297 Chirality : 0.046 0.391 5433 Planarity : 0.004 0.060 6072 Dihedral : 4.696 55.082 4631 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.45 % Allowed : 14.27 % Favored : 83.28 % 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: -1.41 (0.13), residues: 4266 helix: 1.49 (0.21), residues: 665 sheet: -0.58 (0.14), residues: 1218 loop : -1.92 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 59 TYR 0.029 0.001 TYR L 145 PHE 0.039 0.001 PHE B 135 TRP 0.022 0.001 TRP L 40 HIS 0.004 0.001 HIS X 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34641) covalent geometry : angle 0.57907 / 0.29 (47148) SS BOND : bond 0.00319 / 0.21 ( 49) SS BOND : angle 1.50315 / 1.03 ( 98) hydrogen bonds : bond 0.04162 / 2.76 ( 1273) hydrogen bonds : angle 5.55852 / 3.82 ( 3495) link_NAG-ASN : bond 0.00325 / 0.22 ( 27) link_NAG-ASN : angle 1.71059 / 1.19 ( 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 307 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 215 time to evaluate : 1.345 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: 0.5261 (p0) cc_final: 0.4990 (p0) REVERT: B 343 ASN cc_start: 0.6385 (m-40) cc_final: 0.5867 (t0) REVERT: B 660 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: B 977 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7632 (pp) REVERT: A 212 LEU cc_start: 0.5045 (mt) cc_final: 0.4517 (tt) REVERT: A 392 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: C 1063 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8191 (pp) REVERT: C 1107 ARG cc_start: 0.7647 (ttm170) cc_final: 0.7307 (mtt90) REVERT: L 65 ASP cc_start: 0.6176 (m-30) cc_final: 0.5889 (m-30) REVERT: H 102 MET cc_start: 0.4413 (pmm) cc_final: 0.4054 (pmm) REVERT: H 160 LYS cc_start: 0.2432 (mttm) cc_final: 0.1648 (pttm) REVERT: Y 101 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4100 (mp0) REVERT: E 35 TYR cc_start: 0.1636 (OUTLIER) cc_final: 0.1001 (t80) REVERT: F 43 LYS cc_start: 0.3299 (mmtm) cc_final: 0.2293 (tmtt) REVERT: F 214 ASN cc_start: 0.1785 (OUTLIER) cc_final: 0.1341 (t0) outliers start: 92 outliers final: 63 residues processed: 294 average time/residue: 0.2138 time to fit residues: 104.7324 Evaluate side-chains 256 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 660 TYR Chi-restraints excluded: chain B residue 869 MET 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 859 THR Chi-restraints excluded: chain A residue 950 ASP 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 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 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1096 VAL 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 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 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 65 LYS 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: 30.0000 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 141 optimal weight: 0.0020 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4619 r_free = 0.4619 target = 0.191412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.163335 restraints weight = 67297.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.158147 restraints weight = 101959.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155638 restraints weight = 92240.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.155012 restraints weight = 77811.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.152892 restraints weight = 65570.928| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2546 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= 0.171 Angle : 0.632 11.754 47327 Z= 0.321 Chirality : 0.048 0.410 5433 Planarity : 0.004 0.060 6072 Dihedral : 4.838 55.031 4631 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.29 % Allowed : 15.31 % Favored : 82.40 % 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: -1.48 (0.13), residues: 4266 helix: 1.24 (0.20), residues: 662 sheet: -0.57 (0.14), residues: 1225 loop : -1.93 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.021 0.001 TYR C1067 PHE 0.038 0.002 PHE B 135 TRP 0.017 0.001 TRP L 40 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (34641) covalent geometry : angle 0.62399 / 0.32 (47148) SS BOND : bond 0.00351 / 0.23 ( 49) SS BOND : angle 1.62807 / 1.11 ( 98) hydrogen bonds : bond 0.04797 / 3.19 ( 1273) hydrogen bonds : angle 5.65291 / 3.88 ( 3495) link_NAG-ASN : bond 0.00257 / 0.18 ( 27) link_NAG-ASN : angle 1.89381 / 1.30 ( 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 275 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 189 time to evaluate : 1.319 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 111 ASP cc_start: 0.5397 (p0) cc_final: 0.5051 (p0) REVERT: B 343 ASN cc_start: 0.6355 (m-40) cc_final: 0.5847 (t0) REVERT: B 660 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: B 722 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8913 (m) REVERT: B 740 MET cc_start: 0.8287 (tpt) cc_final: 0.7851 (tpp) REVERT: B 977 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7652 (pp) REVERT: A 212 LEU cc_start: 0.4953 (mt) cc_final: 0.4472 (tt) REVERT: A 392 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: C 900 MET cc_start: 0.7924 (mtp) cc_final: 0.7553 (mtp) REVERT: C 1107 ARG cc_start: 0.7730 (ttm170) cc_final: 0.7354 (mtt90) REVERT: H 102 MET cc_start: 0.4525 (pmm) cc_final: 0.4175 (pmm) REVERT: H 134 LYS cc_start: 0.2306 (ptmm) cc_final: 0.0985 (ptpt) REVERT: H 160 LYS cc_start: 0.2975 (mttm) cc_final: 0.2006 (pttm) REVERT: Y 101 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4165 (mp0) REVERT: E 4 MET cc_start: 0.2476 (tpp) cc_final: 0.2181 (tpp) REVERT: E 35 TYR cc_start: 0.1887 (OUTLIER) cc_final: 0.1168 (t80) REVERT: F 43 LYS cc_start: 0.3447 (mmtm) cc_final: 0.2197 (tmtt) REVERT: F 214 ASN cc_start: 0.1927 (OUTLIER) cc_final: 0.1451 (t0) outliers start: 86 outliers final: 66 residues processed: 267 average time/residue: 0.2207 time to fit residues: 98.0362 Evaluate side-chains 255 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 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 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 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 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 432 CYS Chi-restraints excluded: chain C residue 530 SER 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 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 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 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 65 LYS 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: 6.9990 chunk 166 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 347 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4640 r_free = 0.4640 target = 0.193313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.166574 restraints weight = 67016.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.161318 restraints weight = 92160.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.158258 restraints weight = 79246.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157042 restraints weight = 80223.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155273 restraints weight = 66137.738| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34717 Z= 0.115 Angle : 0.589 11.834 47327 Z= 0.297 Chirality : 0.046 0.393 5433 Planarity : 0.004 0.060 6072 Dihedral : 4.664 55.111 4631 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.32 % Allowed : 15.55 % Favored : 82.14 % 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: -1.35 (0.13), residues: 4266 helix: 1.40 (0.20), residues: 672 sheet: -0.47 (0.15), residues: 1210 loop : -1.88 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 66 TYR 0.019 0.001 TYR C1067 PHE 0.034 0.001 PHE B 135 TRP 0.017 0.001 TRP L 40 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (34641) covalent geometry : angle 0.58210 / 0.29 (47148) SS BOND : bond 0.00305 / 0.20 ( 49) SS BOND : angle 1.46996 / 1.02 ( 98) hydrogen bonds : bond 0.04235 / 2.82 ( 1273) hydrogen bonds : angle 5.45625 / 3.74 ( 3495) link_NAG-ASN : bond 0.00298 / 0.20 ( 27) link_NAG-ASN : angle 1.70001 / 1.17 ( 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 283 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 196 time to evaluate : 1.587 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 343 ASN cc_start: 0.6272 (m-40) cc_final: 0.5814 (t0) REVERT: B 722 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8835 (m) REVERT: B 977 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7641 (pp) REVERT: C 1063 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8126 (pp) REVERT: C 1107 ARG cc_start: 0.7652 (ttm170) cc_final: 0.7290 (mtt90) REVERT: H 102 MET cc_start: 0.4522 (pmm) cc_final: 0.4173 (pmm) REVERT: H 134 LYS cc_start: 0.2284 (ptmm) cc_final: 0.0978 (ptpt) REVERT: H 160 LYS cc_start: 0.3007 (mttm) cc_final: 0.2167 (pttp) REVERT: Y 101 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4300 (mp0) REVERT: Y 120 TRP cc_start: 0.5361 (OUTLIER) cc_final: 0.4996 (m-90) REVERT: Y 160 LYS cc_start: 0.1530 (tptt) cc_final: 0.1294 (tptt) REVERT: E 4 MET cc_start: 0.2686 (tpp) cc_final: 0.2234 (tpp) REVERT: E 35 TYR cc_start: 0.1912 (OUTLIER) cc_final: 0.1203 (t80) REVERT: F 43 LYS cc_start: 0.3405 (mmtm) cc_final: 0.2218 (tmtt) outliers start: 87 outliers final: 64 residues processed: 273 average time/residue: 0.2154 time to fit residues: 98.9062 Evaluate side-chains 254 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 722 VAL Chi-restraints excluded: chain B residue 945 LEU 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 207 HIS 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 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 130 VAL Chi-restraints excluded: chain C residue 205 SER 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 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 571 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 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 215 VAL 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 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 65 LYS Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 403 optimal weight: 40.0000 chunk 340 optimal weight: 0.0270 chunk 197 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 391 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 0.0470 chunk 309 optimal weight: 20.0000 chunk 414 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 276 optimal weight: 0.0770 overall best weight: 1.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.193123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.164814 restraints weight = 66592.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.159852 restraints weight = 100197.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.156478 restraints weight = 78140.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.154166 restraints weight = 74957.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.153683 restraints weight = 57432.444| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34717 Z= 0.125 Angle : 0.604 11.754 47327 Z= 0.305 Chirality : 0.046 0.392 5433 Planarity : 0.005 0.081 6072 Dihedral : 4.668 55.095 4631 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.26 % Allowed : 15.87 % Favored : 81.87 % 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: -1.30 (0.13), residues: 4266 helix: 1.39 (0.20), residues: 672 sheet: -0.42 (0.15), residues: 1212 loop : -1.85 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 214 TYR 0.019 0.001 TYR C1067 PHE 0.034 0.001 PHE B 135 TRP 0.025 0.001 TRP L 40 HIS 0.006 0.001 HIS X 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (34641) covalent geometry : angle 0.59625 / 0.30 (47148) SS BOND : bond 0.00309 / 0.21 ( 49) SS BOND : angle 1.57796 / 1.09 ( 98) hydrogen bonds : bond 0.04271 / 2.83 ( 1273) hydrogen bonds : angle 5.45243 / 3.73 ( 3495) link_NAG-ASN : bond 0.00255 / 0.17 ( 27) link_NAG-ASN : angle 1.73805 / 1.19 ( 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 279 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 194 time to evaluate : 1.445 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 343 ASN cc_start: 0.6457 (m-40) cc_final: 0.5931 (t0) REVERT: B 722 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8826 (m) REVERT: B 977 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7641 (pp) REVERT: A 392 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: C 1063 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7970 (pp) REVERT: C 1107 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7382 (mtt90) REVERT: H 134 LYS cc_start: 0.2472 (ptmm) cc_final: 0.1160 (ptpt) REVERT: H 160 LYS cc_start: 0.2743 (mttm) cc_final: 0.1958 (pttm) REVERT: X 54 TYR cc_start: 0.5037 (t80) cc_final: 0.4262 (t80) REVERT: Y 101 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4279 (mp0) REVERT: E 4 MET cc_start: 0.2657 (tpp) cc_final: 0.2311 (tpp) REVERT: E 35 TYR cc_start: 0.1736 (OUTLIER) cc_final: 0.1121 (t80) REVERT: F 43 LYS cc_start: 0.3554 (mmtm) cc_final: 0.2364 (tmtt) outliers start: 85 outliers final: 69 residues processed: 265 average time/residue: 0.1968 time to fit residues: 88.6692 Evaluate side-chains 255 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 180 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 722 VAL Chi-restraints excluded: chain B residue 945 LEU 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 207 HIS 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 697 MET 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 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER 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 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 4 LEU 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 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 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 65 LYS Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 74 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 409 optimal weight: 9.9990 chunk 224 optimal weight: 0.1980 chunk 244 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4610 r_free = 0.4610 target = 0.190778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.163970 restraints weight = 67284.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.158224 restraints weight = 92766.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.155578 restraints weight = 82702.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154725 restraints weight = 76804.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152066 restraints weight = 71592.030| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 34717 Z= 0.207 Angle : 0.676 12.095 47327 Z= 0.344 Chirality : 0.049 0.424 5433 Planarity : 0.005 0.069 6072 Dihedral : 4.962 55.202 4631 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.13 % Allowed : 16.16 % Favored : 81.71 % 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: -1.48 (0.13), residues: 4266 helix: 1.05 (0.20), residues: 663 sheet: -0.52 (0.15), residues: 1220 loop : -1.89 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 214 TYR 0.025 0.002 TYR B 170 PHE 0.035 0.002 PHE B 135 TRP 0.025 0.002 TRP L 40 HIS 0.005 0.001 HIS X 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (34641) covalent geometry : angle 0.66633 / 0.34 (47148) SS BOND : bond 0.00391 / 0.26 ( 49) SS BOND : angle 1.94277 / 1.30 ( 98) hydrogen bonds : bond 0.05212 / 3.47 ( 1273) hydrogen bonds : angle 5.72402 / 3.92 ( 3495) link_NAG-ASN : bond 0.00256 / 0.18 ( 27) link_NAG-ASN : angle 2.09147 / 1.41 ( 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 260 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 180 time to evaluate : 1.236 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: 0.6341 (m-40) cc_final: 0.5890 (t0) REVERT: B 660 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: B 722 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9002 (m) REVERT: B 740 MET cc_start: 0.8177 (tpt) cc_final: 0.7775 (tpp) REVERT: B 977 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7752 (pp) REVERT: A 392 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: C 900 MET cc_start: 0.7487 (mtp) cc_final: 0.7109 (mtp) REVERT: C 950 ASP cc_start: 0.7040 (p0) cc_final: 0.6778 (p0) REVERT: C 1107 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7404 (mtt90) REVERT: H 134 LYS cc_start: 0.2182 (ptmm) cc_final: 0.0765 (ptpt) REVERT: H 160 LYS cc_start: 0.3091 (mttm) cc_final: 0.2135 (pttm) REVERT: X 54 TYR cc_start: 0.5129 (t80) cc_final: 0.4876 (t80) REVERT: Y 101 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.4377 (mp0) REVERT: E 4 MET cc_start: 0.2643 (tpp) cc_final: 0.2264 (tpp) REVERT: E 35 TYR cc_start: 0.2309 (OUTLIER) cc_final: 0.1685 (t80) REVERT: F 43 LYS cc_start: 0.3541 (mmtm) cc_final: 0.2271 (tmtt) outliers start: 80 outliers final: 71 residues processed: 253 average time/residue: 0.2057 time to fit residues: 87.0137 Evaluate side-chains 249 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 660 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 945 LEU 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 697 MET 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 130 VAL Chi-restraints excluded: chain C residue 205 SER 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 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 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 4 LEU 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 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 65 LYS Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 121 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 232 optimal weight: 20.0000 chunk 71 optimal weight: 0.1980 chunk 112 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 330 optimal weight: 30.0000 chunk 422 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4595 r_free = 0.4595 target = 0.185401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.156439 restraints weight = 65580.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149571 restraints weight = 110981.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.145811 restraints weight = 100874.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.146195 restraints weight = 90900.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145722 restraints weight = 62568.192| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 34717 Z= 0.217 Angle : 0.685 11.276 47327 Z= 0.349 Chirality : 0.049 0.427 5433 Planarity : 0.005 0.062 6072 Dihedral : 5.066 55.421 4631 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.18 % Allowed : 16.32 % Favored : 81.50 % 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: -1.56 (0.13), residues: 4266 helix: 0.93 (0.20), residues: 663 sheet: -0.57 (0.15), residues: 1221 loop : -1.94 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 214 TYR 0.025 0.002 TYR B 170 PHE 0.035 0.002 PHE B 135 TRP 0.014 0.002 TRP H 36 HIS 0.006 0.001 HIS X 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (34641) covalent geometry : angle 0.67534 / 0.35 (47148) SS BOND : bond 0.00397 / 0.26 ( 49) SS BOND : angle 1.83515 / 1.25 ( 98) hydrogen bonds : bond 0.05348 / 3.56 ( 1273) hydrogen bonds : angle 5.79555 / 3.96 ( 3495) link_NAG-ASN : bond 0.00251 / 0.17 ( 27) link_NAG-ASN : angle 2.14516 / 1.45 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.98 seconds wall clock time: 101 minutes 22.66 seconds (6082.66 seconds total)