Starting phenix.real_space_refine on Fri Mar 6 20:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9o_31034/03_2026/7e9o_31034.map" } resolution = 3.41 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 197 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "O" 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: "P" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.29, per 1000 atoms: 0.22 Number of scatterers: 33876 At special positions: 0 Unit cell: (203.67, 199.29, 226.665, 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 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 199 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 157 " - pdb=" SG CYS P 213 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1098 " " 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 A1074 " " 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 B1098 " " NAG B1309 " - " ASN B 331 " " 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: 2.63 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: 77 helices and 75 sheets defined 19.3% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.316A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.708A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.080A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (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 897 through 908 removed outlier: 3.569A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.302A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.444A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 4.011A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.932A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.329A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.076A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.541A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.789A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.918A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.663A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.523A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.708A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.583A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.187A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.772A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.942A pdb=" N GLY C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.714A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.943A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.625A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.914A 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 removed outlier: 3.501A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.602A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.599A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.473A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.155A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.048A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.061A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.915A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.192A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 187 through 194 removed outlier: 3.582A pdb=" N LYS O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'P' and resid 202 through 206 removed outlier: 3.625A pdb=" N LEU P 206 " --> pdb=" O SER P 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.624A pdb=" N VAL X 88 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 133 Processing helix chain 'X' and resid 187 through 194 Processing helix chain 'Y' and resid 173 through 175 No H-bonds generated for 'chain 'Y' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.773A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 4.134A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.605A 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: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.577A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.192A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.833A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.040A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.171A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.982A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.625A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.828A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.877A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.359A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.550A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.943A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.061A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 3.921A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.585A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 119 through 123 removed outlier: 6.206A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.148A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 137 through 141 Processing sheet with id=AG1, first strand: chain 'H' and resid 137 through 141 removed outlier: 4.038A pdb=" N SER H 194 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 168 through 171 removed outlier: 4.321A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'O' and resid 58 through 59 removed outlier: 6.331A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR O 54 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU O 38 " --> pdb=" O TYR O 54 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 119 through 123 removed outlier: 5.817A pdb=" N TYR O 178 " --> pdb=" O ASN O 143 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 158 through 160 removed outlier: 4.352A pdb=" N TRP O 153 " --> pdb=" O GLN O 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'P' and resid 46 through 51 removed outlier: 5.092A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS P 98 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 119 " --> pdb=" O LYS P 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH1, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH2, first strand: chain 'P' and resid 168 through 171 Processing sheet with id=AH3, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH4, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.630A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 119 through 123 removed outlier: 4.129A pdb=" N ASN X 143 " --> pdb=" O TYR X 178 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR X 178 " --> pdb=" O ASN X 143 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER X 179 " --> pdb=" O THR X 169 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.386A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.632A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI2, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI3, first strand: chain 'Y' and resid 168 through 171 removed outlier: 4.326A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) 1372 hydrogen bonds defined for protein. 3648 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: 9.94 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5564 1.31 - 1.44: 9451 1.44 - 1.57: 19437 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" C7 NAG C1303 " pdb=" N2 NAG C1303 " ideal model delta sigma weight residual 1.346 1.466 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG B1304 " pdb=" N2 NAG B1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 45596 2.08 - 4.17: 1308 4.17 - 6.25: 217 6.25 - 8.33: 19 8.33 - 10.41: 8 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE A 909 " pdb=" CA ILE A 909 " pdb=" C ILE A 909 " ideal model delta sigma weight residual 111.88 102.35 9.53 1.06e+00 8.90e-01 8.08e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" C PRO C 942 " ideal model delta sigma weight residual 113.40 123.72 -10.32 1.34e+00 5.57e-01 5.94e+01 angle pdb=" C PHE B 906 " pdb=" CA PHE B 906 " pdb=" CB PHE B 906 " ideal model delta sigma weight residual 110.90 100.49 10.41 1.58e+00 4.01e-01 4.34e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" C PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 111.46 103.53 7.93 1.29e+00 6.01e-01 3.78e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 19848 24.09 - 48.18: 895 48.18 - 72.27: 150 72.27 - 96.36: 55 96.36 - 120.45: 79 Dihedral angle restraints: 21027 sinusoidal: 8475 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.95 -90.05 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.07 86.07 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 ... (remaining 21024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4999 0.093 - 0.187: 404 0.187 - 0.280: 25 0.280 - 0.374: 2 0.374 - 0.467: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA PHE B 898 " pdb=" N PHE B 898 " pdb=" C PHE B 898 " pdb=" CB PHE B 898 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 897 " 0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO B 897 " -0.071 2.00e-02 2.50e+03 pdb=" O PRO B 897 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE B 898 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 740 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C MET B 740 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 740 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR B 741 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C THR B 887 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.019 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2777 2.74 - 3.28: 33288 3.28 - 3.82: 52847 3.82 - 4.36: 61784 4.36 - 4.90: 108254 Nonbonded interactions: 258950 Sorted by model distance: nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.202 3.120 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.206 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASN A 282 " pdb=" O3 NAG A1301 " model vdw 2.221 3.040 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.222 3.120 ... (remaining 258945 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.930 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 0.120 34717 Z= 0.355 Angle : 0.831 10.414 47327 Z= 0.475 Chirality : 0.052 0.467 5433 Planarity : 0.005 0.072 6072 Dihedral : 16.683 120.447 12816 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.24 % Allowed : 0.80 % Favored : 98.96 % 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: -1.55 (0.12), residues: 4266 helix: 0.47 (0.20), residues: 657 sheet: -0.40 (0.15), residues: 1194 loop : -1.85 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 67 TYR 0.021 0.001 TYR H 211 PHE 0.036 0.002 PHE A 888 TRP 0.020 0.002 TRP C 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00660 (34641) covalent geometry : angle 0.81951 (47148) SS BOND : bond 0.00385 ( 49) SS BOND : angle 1.90065 ( 98) hydrogen bonds : bond 0.13937 ( 1321) hydrogen bonds : angle 7.20307 ( 3648) link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 2.80234 ( 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 351 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 342 time to evaluate : 1.100 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: symmetry clash REVERT: B 244 LEU cc_start: 0.6116 (tp) cc_final: 0.5800 (pt) REVERT: B 740 MET cc_start: 0.8076 (mmt) cc_final: 0.7741 (mmm) REVERT: B 823 PHE cc_start: 0.7491 (m-80) cc_final: 0.7272 (m-80) REVERT: B 902 MET cc_start: 0.8350 (tpt) cc_final: 0.8075 (mmt) REVERT: B 950 ASP cc_start: 0.8412 (p0) cc_final: 0.8106 (p0) REVERT: A 129 LYS cc_start: 0.7191 (tmtt) cc_final: 0.6730 (tptp) REVERT: A 237 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7277 (mtm110) REVERT: A 399 SER cc_start: 0.6735 (m) cc_final: 0.6517 (m) REVERT: A 400 PHE cc_start: 0.7566 (p90) cc_final: 0.7226 (p90) REVERT: A 983 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7603 (ptt90) REVERT: A 1001 LEU cc_start: 0.8444 (pp) cc_final: 0.8205 (tp) REVERT: A 1142 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7503 (tt0) REVERT: C 215 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6329 (t70) REVERT: C 287 ASP cc_start: 0.7961 (t0) cc_final: 0.7480 (m-30) REVERT: C 740 MET cc_start: 0.8530 (tpt) cc_final: 0.8171 (mtt) REVERT: H 30 ASP cc_start: 0.7664 (m-30) cc_final: 0.7162 (m-30) REVERT: H 60 TYR cc_start: 0.5903 (m-80) cc_final: 0.5634 (m-80) REVERT: O 94 MET cc_start: 0.4423 (tmm) cc_final: 0.4105 (tmm) REVERT: P 39 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6253 (tt0) REVERT: P 46 GLU cc_start: 0.4539 (mm-30) cc_final: 0.4312 (pp20) REVERT: P 65 LYS cc_start: 0.3520 (tttt) cc_final: 0.2427 (mttt) REVERT: P 98 LYS cc_start: 0.3970 (ptmt) cc_final: 0.3348 (mmtp) REVERT: P 102 MET cc_start: 0.6825 (ppp) cc_final: 0.5352 (mpp) REVERT: P 132 SER cc_start: 0.5232 (OUTLIER) cc_final: 0.5002 (t) REVERT: X 31 HIS cc_start: 0.6544 (t70) cc_final: 0.6016 (t70) REVERT: X 101 PHE cc_start: 0.7332 (m-10) cc_final: 0.7073 (m-10) REVERT: Y 31 ASP cc_start: 0.8754 (m-30) cc_final: 0.8532 (t70) REVERT: Y 227 LYS cc_start: 0.3225 (tmtt) cc_final: 0.2772 (ttmt) outliers start: 9 outliers final: 1 residues processed: 349 average time/residue: 0.2005 time to fit residues: 115.7001 Evaluate side-chains 220 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Y residue 201 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 0.4980 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 935 GLN A 450 ASN A 487 ASN A 658 ASN A 751 ASN A 804 GLN A 907 ASN C 762 GLN L 31 HIS ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 ASN Y 35 HIS ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121948 restraints weight = 58471.000| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.62 r_work: 0.3187 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34717 Z= 0.149 Angle : 0.666 10.388 47327 Z= 0.332 Chirality : 0.048 0.267 5433 Planarity : 0.005 0.053 6072 Dihedral : 11.690 102.599 5200 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.67 % Allowed : 6.55 % Favored : 92.78 % 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: -1.16 (0.13), residues: 4266 helix: 1.23 (0.20), residues: 649 sheet: -0.35 (0.15), residues: 1219 loop : -1.61 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 72 TYR 0.026 0.001 TYR Y 162 PHE 0.031 0.002 PHE B 168 TRP 0.014 0.002 TRP C 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00354 (34641) covalent geometry : angle 0.65013 (47148) SS BOND : bond 0.00579 ( 49) SS BOND : angle 1.79145 ( 98) hydrogen bonds : bond 0.04958 ( 1321) hydrogen bonds : angle 5.80411 ( 3648) link_NAG-ASN : bond 0.00403 ( 27) link_NAG-ASN : angle 3.02073 ( 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 266 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 1.214 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 244 LEU cc_start: 0.6200 (tp) cc_final: 0.5807 (pt) REVERT: B 823 PHE cc_start: 0.7876 (m-80) cc_final: 0.7572 (m-80) REVERT: B 981 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (mm) REVERT: A 129 LYS cc_start: 0.7338 (tmtt) cc_final: 0.6931 (tmtt) REVERT: A 237 ARG cc_start: 0.7755 (ptm-80) cc_final: 0.7511 (mtm-85) REVERT: A 399 SER cc_start: 0.6613 (m) cc_final: 0.6331 (m) REVERT: A 400 PHE cc_start: 0.7471 (p90) cc_final: 0.7113 (p90) REVERT: A 974 SER cc_start: 0.9143 (t) cc_final: 0.8907 (t) REVERT: A 1001 LEU cc_start: 0.8196 (pp) cc_final: 0.7944 (tp) REVERT: A 1142 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7476 (tt0) REVERT: C 287 ASP cc_start: 0.8444 (t0) cc_final: 0.7443 (m-30) REVERT: C 740 MET cc_start: 0.8906 (tpt) cc_final: 0.8173 (mtt) REVERT: C 1114 ILE cc_start: 0.8837 (tp) cc_final: 0.8551 (mt) REVERT: L 123 PHE cc_start: 0.4412 (m-80) cc_final: 0.3991 (m-80) REVERT: H 32 TYR cc_start: 0.6576 (m-10) cc_final: 0.6221 (m-80) REVERT: H 39 GLN cc_start: 0.5150 (tm-30) cc_final: 0.4819 (tm-30) REVERT: H 60 TYR cc_start: 0.5542 (m-80) cc_final: 0.5235 (m-80) REVERT: H 95 TYR cc_start: 0.4940 (m-80) cc_final: 0.4479 (m-10) REVERT: P 46 GLU cc_start: 0.4700 (mm-30) cc_final: 0.4431 (pp20) REVERT: P 65 LYS cc_start: 0.2554 (tttt) cc_final: 0.1800 (mttt) REVERT: P 98 LYS cc_start: 0.4322 (ptmt) cc_final: 0.3633 (mmtp) REVERT: P 102 MET cc_start: 0.6828 (ppp) cc_final: 0.5422 (mpp) REVERT: X 31 HIS cc_start: 0.6348 (t70) cc_final: 0.6063 (t70) REVERT: X 101 PHE cc_start: 0.7060 (m-10) cc_final: 0.6815 (m-10) REVERT: Y 30 ASP cc_start: 0.7576 (m-30) cc_final: 0.7349 (m-30) REVERT: Y 31 ASP cc_start: 0.8919 (m-30) cc_final: 0.8539 (t70) REVERT: Y 83 MET cc_start: 0.3361 (mpp) cc_final: 0.3156 (mpp) outliers start: 25 outliers final: 15 residues processed: 259 average time/residue: 0.2057 time to fit residues: 88.2074 Evaluate side-chains 226 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain Y residue 102 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 17 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 415 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 133 optimal weight: 50.0000 chunk 229 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN A 949 GLN H 77 ASN P 54 ASN Y 3 GLN ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.184754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117735 restraints weight = 58117.115| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.42 r_work: 0.3151 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 34717 Z= 0.196 Angle : 0.681 10.525 47327 Z= 0.341 Chirality : 0.048 0.296 5433 Planarity : 0.005 0.053 6072 Dihedral : 8.662 94.228 5196 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.33 % Allowed : 9.35 % Favored : 89.32 % 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: -1.15 (0.13), residues: 4266 helix: 1.17 (0.20), residues: 648 sheet: -0.28 (0.15), residues: 1194 loop : -1.61 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.021 0.002 TYR A1067 PHE 0.029 0.002 PHE B 168 TRP 0.019 0.002 TRP L 40 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00486 (34641) covalent geometry : angle 0.66426 (47148) SS BOND : bond 0.00492 ( 49) SS BOND : angle 1.87477 ( 98) hydrogen bonds : bond 0.05349 ( 1321) hydrogen bonds : angle 5.69708 ( 3648) link_NAG-ASN : bond 0.00401 ( 27) link_NAG-ASN : angle 3.12327 ( 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 284 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6002 (tp) cc_final: 0.5686 (pt) REVERT: B 823 PHE cc_start: 0.8165 (m-80) cc_final: 0.7886 (m-80) REVERT: A 237 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7591 (mtp-110) REVERT: A 399 SER cc_start: 0.6645 (m) cc_final: 0.6362 (m) REVERT: A 400 PHE cc_start: 0.7499 (p90) cc_final: 0.7040 (p90) REVERT: A 423 TYR cc_start: 0.5774 (t80) cc_final: 0.5553 (t80) REVERT: A 773 GLU cc_start: 0.8472 (tp30) cc_final: 0.8021 (tt0) REVERT: A 957 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7649 (mt0) REVERT: A 974 SER cc_start: 0.8997 (t) cc_final: 0.8794 (t) REVERT: A 1001 LEU cc_start: 0.8441 (pp) cc_final: 0.8132 (tp) REVERT: A 1142 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7539 (tt0) REVERT: C 287 ASP cc_start: 0.8650 (t0) cc_final: 0.7667 (m-30) REVERT: C 740 MET cc_start: 0.9033 (tpt) cc_final: 0.8254 (mtt) REVERT: C 1031 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: C 1114 ILE cc_start: 0.8858 (tp) cc_final: 0.8583 (mt) REVERT: C 1145 LEU cc_start: 0.7224 (mm) cc_final: 0.6930 (mm) REVERT: L 123 PHE cc_start: 0.5108 (m-80) cc_final: 0.4684 (m-80) REVERT: L 139 CYS cc_start: 0.3813 (t) cc_final: 0.3597 (t) REVERT: L 178 TYR cc_start: 0.5592 (m-10) cc_final: 0.5165 (m-10) REVERT: P 46 GLU cc_start: 0.4718 (mm-30) cc_final: 0.4378 (pp20) REVERT: P 98 LYS cc_start: 0.4320 (ptmt) cc_final: 0.3660 (mmmm) REVERT: P 102 MET cc_start: 0.6807 (ppp) cc_final: 0.5366 (mpp) REVERT: X 31 HIS cc_start: 0.6265 (t70) cc_final: 0.5992 (t70) REVERT: X 101 PHE cc_start: 0.7094 (m-10) cc_final: 0.6814 (m-10) REVERT: Y 31 ASP cc_start: 0.8965 (m-30) cc_final: 0.8416 (p0) REVERT: Y 134 LYS cc_start: 0.4944 (tptp) cc_final: 0.4468 (mttt) outliers start: 50 outliers final: 28 residues processed: 272 average time/residue: 0.1998 time to fit residues: 90.5778 Evaluate side-chains 240 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain Y residue 102 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 161 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 291 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 402 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN B 935 GLN A 414 GLN L 31 HIS H 77 ASN P 39 GLN Y 209 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118261 restraints weight = 57835.544| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 4.55 r_work: 0.3188 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34717 Z= 0.131 Angle : 0.609 11.939 47327 Z= 0.305 Chirality : 0.046 0.309 5433 Planarity : 0.004 0.054 6072 Dihedral : 7.490 89.672 5196 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.89 % Allowed : 10.57 % Favored : 87.54 % 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: -0.93 (0.13), residues: 4266 helix: 1.39 (0.20), residues: 659 sheet: -0.20 (0.15), residues: 1213 loop : -1.46 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 72 TYR 0.018 0.001 TYR H 32 PHE 0.028 0.001 PHE B 168 TRP 0.015 0.001 TRP H 53 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00311 (34641) covalent geometry : angle 0.59139 (47148) SS BOND : bond 0.00398 ( 49) SS BOND : angle 1.71457 ( 98) hydrogen bonds : bond 0.04534 ( 1321) hydrogen bonds : angle 5.39572 ( 3648) link_NAG-ASN : bond 0.00415 ( 27) link_NAG-ASN : angle 3.08517 ( 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: 71 poor density : 234 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7114 (m-80) cc_final: 0.6826 (m-10) REVERT: B 244 LEU cc_start: 0.6194 (tp) cc_final: 0.5830 (pt) REVERT: B 551 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6555 (p) REVERT: B 811 LYS cc_start: 0.7818 (mttm) cc_final: 0.7172 (mttm) REVERT: B 823 PHE cc_start: 0.8159 (m-80) cc_final: 0.7821 (m-80) REVERT: A 399 SER cc_start: 0.6571 (m) cc_final: 0.6271 (m) REVERT: A 400 PHE cc_start: 0.7515 (p90) cc_final: 0.7018 (p90) REVERT: A 957 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7669 (mt0) REVERT: A 974 SER cc_start: 0.8949 (t) cc_final: 0.8548 (t) REVERT: A 983 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7742 (ptt-90) REVERT: A 1001 LEU cc_start: 0.8270 (pp) cc_final: 0.8048 (tp) REVERT: A 1142 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7590 (tt0) REVERT: C 287 ASP cc_start: 0.8658 (t0) cc_final: 0.7682 (m-30) REVERT: C 740 MET cc_start: 0.8987 (tpt) cc_final: 0.8189 (mtt) REVERT: C 945 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7595 (pt) REVERT: C 1031 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: C 1061 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8785 (m) REVERT: C 1114 ILE cc_start: 0.8809 (tp) cc_final: 0.8559 (mt) REVERT: C 1145 LEU cc_start: 0.7311 (mm) cc_final: 0.7007 (mm) REVERT: L 121 PHE cc_start: 0.5008 (m-80) cc_final: 0.4679 (t80) REVERT: L 178 TYR cc_start: 0.5716 (m-10) cc_final: 0.5274 (m-10) REVERT: H 60 TYR cc_start: 0.5985 (m-80) cc_final: 0.5476 (m-80) REVERT: H 87 ARG cc_start: 0.7068 (tpp-160) cc_final: 0.6712 (mmt180) REVERT: H 117 MET cc_start: 0.3220 (OUTLIER) cc_final: 0.1974 (mmm) REVERT: O 51 LEU cc_start: 0.2723 (OUTLIER) cc_final: 0.1995 (tt) REVERT: P 46 GLU cc_start: 0.4870 (mm-30) cc_final: 0.4620 (pp20) REVERT: P 98 LYS cc_start: 0.4364 (ptmt) cc_final: 0.3758 (mmmm) REVERT: P 102 MET cc_start: 0.7029 (ppp) cc_final: 0.5701 (mpp) REVERT: X 31 HIS cc_start: 0.6333 (t70) cc_final: 0.6069 (t70) REVERT: X 101 PHE cc_start: 0.7111 (m-10) cc_final: 0.6885 (m-10) REVERT: Y 31 ASP cc_start: 0.8991 (m-30) cc_final: 0.8453 (p0) REVERT: Y 134 LYS cc_start: 0.4868 (tptp) cc_final: 0.4367 (mttt) outliers start: 71 outliers final: 42 residues processed: 293 average time/residue: 0.1937 time to fit residues: 96.0550 Evaluate side-chains 260 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain Y residue 30 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 1 optimal weight: 0.9990 chunk 315 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 383 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN L 31 HIS H 77 ASN P 39 GLN ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.186769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119583 restraints weight = 58337.759| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.15 r_work: 0.3198 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34717 Z= 0.132 Angle : 0.605 12.888 47327 Z= 0.302 Chirality : 0.046 0.311 5433 Planarity : 0.004 0.049 6072 Dihedral : 7.129 86.953 5196 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.26 % Allowed : 11.10 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4266 helix: 1.46 (0.20), residues: 659 sheet: -0.11 (0.15), residues: 1202 loop : -1.41 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.017 0.001 TYR C1067 PHE 0.029 0.001 PHE B 168 TRP 0.015 0.001 TRP H 53 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (34641) covalent geometry : angle 0.58757 (47148) SS BOND : bond 0.00386 ( 49) SS BOND : angle 1.72698 ( 98) hydrogen bonds : bond 0.04472 ( 1321) hydrogen bonds : angle 5.26388 ( 3648) link_NAG-ASN : bond 0.00409 ( 27) link_NAG-ASN : angle 3.04692 ( 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 309 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 224 time to evaluate : 1.212 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 244 LEU cc_start: 0.6145 (tp) cc_final: 0.5760 (pt) REVERT: B 551 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6605 (p) REVERT: B 811 LYS cc_start: 0.7829 (mttm) cc_final: 0.7379 (mttm) REVERT: A 301 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 400 PHE cc_start: 0.7496 (p90) cc_final: 0.7045 (p90) REVERT: A 423 TYR cc_start: 0.5783 (t80) cc_final: 0.5583 (t80) REVERT: A 957 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7723 (mt0) REVERT: A 974 SER cc_start: 0.8888 (t) cc_final: 0.8427 (t) REVERT: A 983 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7629 (ptt-90) REVERT: A 1001 LEU cc_start: 0.8261 (pp) cc_final: 0.8050 (tp) REVERT: A 1142 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7640 (tt0) REVERT: C 56 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7826 (tp) REVERT: C 287 ASP cc_start: 0.8608 (t0) cc_final: 0.7641 (m-30) REVERT: C 740 MET cc_start: 0.8968 (tpt) cc_final: 0.8190 (mtt) REVERT: C 945 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7941 (pp) REVERT: C 1031 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: C 1061 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8796 (m) REVERT: C 1114 ILE cc_start: 0.8805 (tp) cc_final: 0.8567 (mt) REVERT: C 1145 LEU cc_start: 0.7167 (mm) cc_final: 0.6845 (mm) REVERT: L 121 PHE cc_start: 0.5009 (m-80) cc_final: 0.4681 (t80) REVERT: L 178 TYR cc_start: 0.5753 (m-10) cc_final: 0.5333 (m-10) REVERT: H 32 TYR cc_start: 0.7128 (m-10) cc_final: 0.6767 (m-80) REVERT: H 60 TYR cc_start: 0.6272 (m-80) cc_final: 0.5805 (m-80) REVERT: H 87 ARG cc_start: 0.6851 (tpp-160) cc_final: 0.6449 (mmt180) REVERT: H 117 MET cc_start: 0.3256 (OUTLIER) cc_final: 0.2041 (mmm) REVERT: P 65 LYS cc_start: 0.2378 (tttt) cc_final: 0.1549 (mttt) REVERT: P 98 LYS cc_start: 0.4256 (ptmt) cc_final: 0.3724 (mmmm) REVERT: P 102 MET cc_start: 0.7108 (ppp) cc_final: 0.5725 (mpp) REVERT: X 31 HIS cc_start: 0.6285 (t70) cc_final: 0.5996 (t70) REVERT: X 101 PHE cc_start: 0.7136 (m-10) cc_final: 0.6925 (m-10) REVERT: Y 31 ASP cc_start: 0.8957 (m-30) cc_final: 0.8425 (p0) outliers start: 85 outliers final: 49 residues processed: 294 average time/residue: 0.1976 time to fit residues: 98.5764 Evaluate side-chains 265 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 76 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 220 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN L 31 HIS ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 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 = 0.4424 r_free = 0.4424 target = 0.184292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118744 restraints weight = 58560.410| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.58 r_work: 0.3208 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34717 Z= 0.118 Angle : 0.584 13.008 47327 Z= 0.291 Chirality : 0.045 0.318 5433 Planarity : 0.004 0.048 6072 Dihedral : 6.760 84.553 5196 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 11.63 % Favored : 86.29 % 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: -0.72 (0.13), residues: 4266 helix: 1.55 (0.20), residues: 666 sheet: -0.11 (0.15), residues: 1221 loop : -1.31 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.017 0.001 TYR C1067 PHE 0.025 0.001 PHE B 168 TRP 0.012 0.001 TRP H 120 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (34641) covalent geometry : angle 0.56741 (47148) SS BOND : bond 0.00364 ( 49) SS BOND : angle 1.63013 ( 98) hydrogen bonds : bond 0.04208 ( 1321) hydrogen bonds : angle 5.11512 ( 3648) link_NAG-ASN : bond 0.00385 ( 27) link_NAG-ASN : angle 2.92560 ( 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 311 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 1.263 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 244 LEU cc_start: 0.6115 (tp) cc_final: 0.5752 (pt) REVERT: B 551 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6594 (p) REVERT: A 301 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7929 (m) REVERT: A 400 PHE cc_start: 0.7485 (p90) cc_final: 0.7012 (p90) REVERT: A 1142 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7682 (tt0) REVERT: C 287 ASP cc_start: 0.8564 (t0) cc_final: 0.7645 (m-30) REVERT: C 740 MET cc_start: 0.8946 (tpt) cc_final: 0.8202 (mtt) REVERT: C 945 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7692 (pt) REVERT: C 1031 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: C 1061 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8812 (m) REVERT: C 1114 ILE cc_start: 0.8801 (tp) cc_final: 0.8574 (mt) REVERT: C 1145 LEU cc_start: 0.7186 (mm) cc_final: 0.6852 (mm) REVERT: L 53 ILE cc_start: 0.7778 (mp) cc_final: 0.7522 (tt) REVERT: L 121 PHE cc_start: 0.5183 (m-80) cc_final: 0.4757 (t80) REVERT: L 178 TYR cc_start: 0.5679 (m-10) cc_final: 0.5145 (m-10) REVERT: H 32 TYR cc_start: 0.6898 (m-10) cc_final: 0.6602 (m-80) REVERT: H 60 TYR cc_start: 0.6351 (m-80) cc_final: 0.5820 (m-80) REVERT: H 87 ARG cc_start: 0.6798 (tpp-160) cc_final: 0.6406 (mmt180) REVERT: H 117 MET cc_start: 0.3044 (OUTLIER) cc_final: 0.1927 (mmm) REVERT: O 92 TYR cc_start: 0.3449 (OUTLIER) cc_final: 0.2770 (t80) REVERT: P 98 LYS cc_start: 0.4220 (ptmt) cc_final: 0.3695 (mmmm) REVERT: P 102 MET cc_start: 0.6949 (ppp) cc_final: 0.5466 (mpp) REVERT: Y 31 ASP cc_start: 0.8940 (m-30) cc_final: 0.8435 (p0) outliers start: 78 outliers final: 53 residues processed: 300 average time/residue: 0.1978 time to fit residues: 100.7366 Evaluate side-chains 264 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 240 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 352 optimal weight: 30.0000 chunk 269 optimal weight: 1.9990 chunk 380 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 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 = 0.4402 r_free = 0.4402 target = 0.182088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.117289 restraints weight = 58874.589| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.99 r_work: 0.3171 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 34717 Z= 0.182 Angle : 0.644 13.069 47327 Z= 0.323 Chirality : 0.047 0.308 5433 Planarity : 0.004 0.049 6072 Dihedral : 6.889 83.825 5196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.40 % Allowed : 12.06 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4266 helix: 1.31 (0.20), residues: 672 sheet: -0.10 (0.15), residues: 1212 loop : -1.38 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.021 0.001 TYR Y 162 PHE 0.024 0.002 PHE A1121 TRP 0.021 0.002 TRP L 40 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00455 (34641) covalent geometry : angle 0.62614 (47148) SS BOND : bond 0.00471 ( 49) SS BOND : angle 2.07144 ( 98) hydrogen bonds : bond 0.04959 ( 1321) hydrogen bonds : angle 5.26618 ( 3648) link_NAG-ASN : bond 0.00332 ( 27) link_NAG-ASN : angle 3.02819 ( 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 310 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 220 time to evaluate : 1.209 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 244 LEU cc_start: 0.6192 (tp) cc_final: 0.5812 (pt) REVERT: A 228 ASP cc_start: 0.8055 (t0) cc_final: 0.7290 (m-30) REVERT: A 301 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 400 PHE cc_start: 0.7664 (p90) cc_final: 0.7157 (p90) REVERT: A 598 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7639 (mt) REVERT: A 974 SER cc_start: 0.8782 (t) cc_final: 0.8309 (t) REVERT: A 983 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7478 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7706 (tt0) REVERT: C 56 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7733 (tp) REVERT: C 287 ASP cc_start: 0.8568 (t0) cc_final: 0.7644 (m-30) REVERT: C 740 MET cc_start: 0.9008 (tpt) cc_final: 0.8291 (mtt) REVERT: C 945 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 1031 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: C 1061 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8820 (m) REVERT: C 1114 ILE cc_start: 0.8854 (tp) cc_final: 0.8618 (mt) REVERT: C 1145 LEU cc_start: 0.7094 (mm) cc_final: 0.6743 (mm) REVERT: L 40 TRP cc_start: 0.7843 (m100) cc_final: 0.7146 (m100) REVERT: L 121 PHE cc_start: 0.5141 (m-80) cc_final: 0.4764 (t80) REVERT: L 178 TYR cc_start: 0.5370 (m-10) cc_final: 0.4811 (m-10) REVERT: H 32 TYR cc_start: 0.7206 (m-10) cc_final: 0.6929 (m-80) REVERT: H 60 TYR cc_start: 0.6498 (m-80) cc_final: 0.6013 (m-80) REVERT: H 80 TYR cc_start: 0.5806 (m-80) cc_final: 0.5429 (m-10) REVERT: H 117 MET cc_start: 0.3501 (OUTLIER) cc_final: 0.2311 (mmm) REVERT: P 98 LYS cc_start: 0.4223 (ptmt) cc_final: 0.3694 (mmmm) REVERT: Y 31 ASP cc_start: 0.8906 (m-30) cc_final: 0.8370 (p0) outliers start: 90 outliers final: 62 residues processed: 297 average time/residue: 0.1940 time to fit residues: 97.7391 Evaluate side-chains 276 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 72 ARG 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: 2.9990 chunk 244 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 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 = 0.4416 r_free = 0.4416 target = 0.185533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116226 restraints weight = 57614.282| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.51 r_work: 0.3162 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 34717 Z= 0.158 Angle : 0.624 12.761 47327 Z= 0.312 Chirality : 0.046 0.319 5433 Planarity : 0.004 0.051 6072 Dihedral : 6.775 82.810 5196 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.13 % Allowed : 12.89 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4266 helix: 1.37 (0.20), residues: 668 sheet: -0.06 (0.15), residues: 1195 loop : -1.36 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.001 PHE B 168 TRP 0.016 0.001 TRP H 120 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00390 (34641) covalent geometry : angle 0.60726 (47148) SS BOND : bond 0.00473 ( 49) SS BOND : angle 1.85337 ( 98) hydrogen bonds : bond 0.04740 ( 1321) hydrogen bonds : angle 5.21856 ( 3648) link_NAG-ASN : bond 0.00336 ( 27) link_NAG-ASN : angle 2.93875 ( 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 297 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 217 time to evaluate : 1.165 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 244 LEU cc_start: 0.6143 (tp) cc_final: 0.5770 (pt) REVERT: B 614 ASP cc_start: 0.8377 (t0) cc_final: 0.8174 (t0) REVERT: A 228 ASP cc_start: 0.7805 (t0) cc_final: 0.7238 (m-30) REVERT: A 301 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7976 (m) REVERT: A 400 PHE cc_start: 0.7488 (p90) cc_final: 0.6973 (p90) REVERT: A 598 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 974 SER cc_start: 0.8768 (t) cc_final: 0.8248 (t) REVERT: A 983 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7493 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7690 (tt0) REVERT: C 56 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7737 (tp) REVERT: C 287 ASP cc_start: 0.8591 (t0) cc_final: 0.7615 (m-30) REVERT: C 740 MET cc_start: 0.9011 (tpt) cc_final: 0.8237 (mtt) REVERT: C 945 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7955 (pp) REVERT: C 1031 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: C 1061 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 1114 ILE cc_start: 0.8827 (tp) cc_final: 0.8577 (mt) REVERT: C 1145 LEU cc_start: 0.7167 (mm) cc_final: 0.6802 (mm) REVERT: L 94 MET cc_start: 0.5803 (mmt) cc_final: 0.5233 (mmm) REVERT: L 121 PHE cc_start: 0.5183 (m-80) cc_final: 0.4769 (t80) REVERT: L 178 TYR cc_start: 0.5468 (m-10) cc_final: 0.5078 (m-10) REVERT: H 32 TYR cc_start: 0.6828 (m-10) cc_final: 0.6597 (m-80) REVERT: H 60 TYR cc_start: 0.6226 (m-80) cc_final: 0.5730 (m-80) REVERT: H 83 MET cc_start: 0.6936 (mpp) cc_final: 0.6185 (mpp) REVERT: H 87 ARG cc_start: 0.6817 (tpp-160) cc_final: 0.6531 (mmt180) REVERT: H 117 MET cc_start: 0.3026 (OUTLIER) cc_final: 0.2036 (mmm) REVERT: O 92 TYR cc_start: 0.3440 (OUTLIER) cc_final: 0.2798 (t80) REVERT: P 98 LYS cc_start: 0.4156 (ptmt) cc_final: 0.3619 (mmmm) REVERT: X 31 HIS cc_start: 0.5929 (t70) cc_final: 0.5728 (t70) REVERT: X 54 TYR cc_start: 0.6932 (m-80) cc_final: 0.6532 (m-80) REVERT: Y 31 ASP cc_start: 0.8886 (m-30) cc_final: 0.8359 (p0) outliers start: 80 outliers final: 63 residues processed: 286 average time/residue: 0.1984 time to fit residues: 96.4237 Evaluate side-chains 278 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 403 optimal weight: 8.9990 chunk 340 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 391 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 309 optimal weight: 30.0000 chunk 414 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 276 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 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 = 0.4404 r_free = 0.4404 target = 0.183829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116852 restraints weight = 57592.105| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.13 r_work: 0.3141 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 34717 Z= 0.216 Angle : 0.674 12.713 47327 Z= 0.339 Chirality : 0.048 0.323 5433 Planarity : 0.004 0.054 6072 Dihedral : 6.967 82.926 5196 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.32 % Allowed : 13.18 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4266 helix: 1.17 (0.20), residues: 666 sheet: -0.11 (0.15), residues: 1216 loop : -1.43 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.023 0.002 TYR Y 162 PHE 0.028 0.002 PHE A1121 TRP 0.018 0.002 TRP H 120 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00542 (34641) covalent geometry : angle 0.65739 (47148) SS BOND : bond 0.00530 ( 49) SS BOND : angle 1.95857 ( 98) hydrogen bonds : bond 0.05356 ( 1321) hydrogen bonds : angle 5.37047 ( 3648) link_NAG-ASN : bond 0.00334 ( 27) link_NAG-ASN : angle 3.07042 ( 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 300 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 213 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6204 (tp) cc_final: 0.5830 (pt) REVERT: B 614 ASP cc_start: 0.8374 (t0) cc_final: 0.8153 (t0) REVERT: A 168 PHE cc_start: 0.7954 (t80) cc_final: 0.7718 (t80) REVERT: A 228 ASP cc_start: 0.7876 (t0) cc_final: 0.7166 (m-30) REVERT: A 301 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 400 PHE cc_start: 0.7545 (p90) cc_final: 0.7032 (p90) REVERT: A 598 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 974 SER cc_start: 0.8841 (t) cc_final: 0.8377 (t) REVERT: A 983 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7473 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7743 (tt0) REVERT: C 56 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7681 (tp) REVERT: C 287 ASP cc_start: 0.8557 (t0) cc_final: 0.7830 (m-30) REVERT: C 740 MET cc_start: 0.9068 (tpt) cc_final: 0.8429 (mtm) REVERT: C 945 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7936 (pp) REVERT: C 1031 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: C 1061 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 1114 ILE cc_start: 0.8857 (tp) cc_final: 0.8603 (mt) REVERT: C 1145 LEU cc_start: 0.7130 (mm) cc_final: 0.6764 (mm) REVERT: L 121 PHE cc_start: 0.5218 (m-80) cc_final: 0.4788 (t80) REVERT: L 144 PHE cc_start: 0.4125 (p90) cc_final: 0.3654 (p90) REVERT: L 178 TYR cc_start: 0.5520 (m-10) cc_final: 0.4815 (m-10) REVERT: H 32 TYR cc_start: 0.6845 (m-10) cc_final: 0.6626 (m-80) REVERT: H 60 TYR cc_start: 0.6346 (m-80) cc_final: 0.5864 (m-80) REVERT: H 117 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2232 (mmm) REVERT: O 92 TYR cc_start: 0.3490 (OUTLIER) cc_final: 0.2837 (t80) REVERT: P 98 LYS cc_start: 0.4188 (ptmt) cc_final: 0.3623 (mmmm) REVERT: X 31 HIS cc_start: 0.5985 (t70) cc_final: 0.5741 (t70) REVERT: X 54 TYR cc_start: 0.6906 (m-80) cc_final: 0.6518 (m-80) REVERT: Y 31 ASP cc_start: 0.8890 (m-30) cc_final: 0.8356 (p0) outliers start: 87 outliers final: 69 residues processed: 289 average time/residue: 0.1984 time to fit residues: 97.4517 Evaluate side-chains 280 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 72 ARG 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: 7.9990 chunk 309 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 409 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 37 optimal weight: 0.0000 chunk 117 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 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 = 0.4400 r_free = 0.4400 target = 0.183520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116381 restraints weight = 58293.397| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.06 r_work: 0.3136 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 34717 Z= 0.229 Angle : 0.694 12.223 47327 Z= 0.349 Chirality : 0.049 0.343 5433 Planarity : 0.005 0.054 6072 Dihedral : 7.088 83.149 5196 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.24 % Allowed : 13.47 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4266 helix: 1.10 (0.20), residues: 660 sheet: -0.15 (0.15), residues: 1192 loop : -1.46 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.023 0.002 TYR A1067 PHE 0.028 0.002 PHE A1121 TRP 0.018 0.002 TRP H 120 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00576 (34641) covalent geometry : angle 0.67702 (47148) SS BOND : bond 0.00548 ( 49) SS BOND : angle 1.99678 ( 98) hydrogen bonds : bond 0.05508 ( 1321) hydrogen bonds : angle 5.43789 ( 3648) link_NAG-ASN : bond 0.00338 ( 27) link_NAG-ASN : angle 3.10421 ( 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 286 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 202 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.5987 (tp) cc_final: 0.5699 (pt) REVERT: B 614 ASP cc_start: 0.8352 (t0) cc_final: 0.8130 (t0) REVERT: A 168 PHE cc_start: 0.8042 (t80) cc_final: 0.7787 (t80) REVERT: A 228 ASP cc_start: 0.7878 (t0) cc_final: 0.7140 (m-30) REVERT: A 301 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7973 (m) REVERT: A 400 PHE cc_start: 0.7472 (p90) cc_final: 0.7051 (p90) REVERT: A 974 SER cc_start: 0.8896 (t) cc_final: 0.8646 (t) REVERT: A 1142 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7799 (tt0) REVERT: C 56 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7672 (tp) REVERT: C 287 ASP cc_start: 0.8543 (t0) cc_final: 0.7817 (m-30) REVERT: C 740 MET cc_start: 0.9024 (tpt) cc_final: 0.8425 (mtm) REVERT: C 945 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7536 (pp) REVERT: C 1031 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: C 1061 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8805 (m) REVERT: C 1114 ILE cc_start: 0.8871 (tp) cc_final: 0.8614 (mt) REVERT: C 1145 LEU cc_start: 0.7206 (mm) cc_final: 0.6806 (mm) REVERT: L 121 PHE cc_start: 0.5215 (m-80) cc_final: 0.4787 (t80) REVERT: L 144 PHE cc_start: 0.4133 (p90) cc_final: 0.3666 (p90) REVERT: L 178 TYR cc_start: 0.5515 (m-10) cc_final: 0.4830 (m-10) REVERT: H 60 TYR cc_start: 0.6199 (m-80) cc_final: 0.5694 (m-80) REVERT: H 83 MET cc_start: 0.6844 (mpp) cc_final: 0.6023 (mpp) REVERT: H 117 MET cc_start: 0.3016 (OUTLIER) cc_final: 0.2106 (mmm) REVERT: O 92 TYR cc_start: 0.3236 (OUTLIER) cc_final: 0.2607 (t80) REVERT: P 98 LYS cc_start: 0.4064 (ptmt) cc_final: 0.3640 (mmtp) REVERT: X 31 HIS cc_start: 0.6001 (t70) cc_final: 0.5757 (t70) REVERT: X 54 TYR cc_start: 0.6918 (m-80) cc_final: 0.6557 (m-80) REVERT: Y 31 ASP cc_start: 0.8854 (m-30) cc_final: 0.8281 (p0) outliers start: 84 outliers final: 73 residues processed: 279 average time/residue: 0.1875 time to fit residues: 89.5181 Evaluate side-chains 279 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 121 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 309 optimal weight: 20.0000 chunk 232 optimal weight: 40.0000 chunk 71 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 362 optimal weight: 30.0000 chunk 330 optimal weight: 0.8980 chunk 422 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 ASN P 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.184266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115900 restraints weight = 58354.021| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.49 r_work: 0.3210 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34717 Z= 0.111 Angle : 0.595 12.332 47327 Z= 0.298 Chirality : 0.045 0.341 5433 Planarity : 0.004 0.053 6072 Dihedral : 6.527 80.602 5196 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.60 % Allowed : 14.08 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4266 helix: 1.57 (0.20), residues: 666 sheet: -0.03 (0.15), residues: 1184 loop : -1.30 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.022 0.001 TYR C1138 PHE 0.022 0.001 PHE B 168 TRP 0.027 0.002 TRP L 40 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (34641) covalent geometry : angle 0.58054 (47148) SS BOND : bond 0.00394 ( 49) SS BOND : angle 1.64795 ( 98) hydrogen bonds : bond 0.04135 ( 1321) hydrogen bonds : angle 5.11448 ( 3648) link_NAG-ASN : bond 0.00396 ( 27) link_NAG-ASN : angle 2.77787 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14570.96 seconds wall clock time: 247 minutes 56.59 seconds (14876.59 seconds total)