Starting phenix.real_space_refine on Sat Jul 4 22:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwt_23556/07_2026/7lwt_23556.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.086 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 103 5.16 5 C 15167 2.51 5 N 3893 2.21 5 O 4596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23759 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7696 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7710 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7681 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.55, per 1000 atoms: 0.19 Number of scatterers: 23759 At special positions: 0 Unit cell: (131.487, 133.625, 193.489, 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 103 16.00 O 4596 8.00 N 3893 7.00 C 15167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 61 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN B1134 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN C 717 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 789.6 milliseconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 45 sheets defined 27.3% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.005A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.403A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.314A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.838A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.268A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.689A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.529A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.842A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.768A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.634A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.524A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) 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 965 removed outlier: 3.900A 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: 4.545A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.333A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.593A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.494A 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 438 through 443 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.680A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.856A 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: 3.886A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.689A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.540A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.613A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.657A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.222A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.917A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.574A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.699A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.046A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.723A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.596A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.575A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.742A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.924A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.134A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.510A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.762A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.776A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.970A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.131A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.558A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.105A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.816A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.522A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.522A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.427A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.161A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.512A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.333A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.588A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.445A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.810A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.211A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.720A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.270A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.757A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.515A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.745A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.791A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.777A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.902A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.634A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.532A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.532A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.797A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2844 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: 4.41 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6595 1.34 - 1.46: 4248 1.46 - 1.58: 13303 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24273 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.71e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.53e+01 bond pdb=" C4 NAG K 1 " pdb=" O4 NAG K 1 " ideal model delta sigma weight residual 1.409 1.486 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 24268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 28142 2.59 - 5.18: 4716 5.18 - 7.76: 163 7.76 - 10.35: 5 10.35 - 12.94: 5 Bond angle restraints: 33031 Sorted by residual: angle pdb=" CA ASP C 570 " pdb=" CB ASP C 570 " pdb=" CG ASP C 570 " ideal model delta sigma weight residual 112.60 120.67 -8.07 1.00e+00 1.00e+00 6.51e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 132.88 -11.34 1.91e+00 2.74e-01 3.53e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" C CYS C1032 " pdb=" CA CYS C1032 " pdb=" CB CYS C1032 " ideal model delta sigma weight residual 109.28 117.02 -7.74 1.33e+00 5.65e-01 3.39e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 33026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13123 17.90 - 35.80: 710 35.80 - 53.70: 121 53.70 - 71.60: 48 71.60 - 89.51: 22 Dihedral angle restraints: 14024 sinusoidal: 5364 harmonic: 8660 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -169.46 83.46 1 1.00e+01 1.00e-02 8.51e+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 -157.20 71.20 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -151.04 65.04 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 14021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 3912 0.281 - 0.562: 18 0.562 - 0.843: 0 0.843 - 1.124: 0 1.124 - 1.405: 3 Chirality restraints: 3933 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.19e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.85e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.68e+01 ... (remaining 3930 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.198 2.00e-02 2.50e+03 1.03e-01 2.65e+02 pdb=" CG TRP C 886 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.087 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.139 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.128 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " 0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.135 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" CG ASN B 657 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.214 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.129 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" CG ASN B 343 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.216 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " -0.166 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 11796 3.00 - 3.48: 22061 3.48 - 3.95: 38546 3.95 - 4.43: 42455 4.43 - 4.90: 72927 Nonbonded interactions: 187785 Sorted by model distance: nonbonded pdb=" OD1 ASP A 570 " pdb=" OG1 THR A 572 " model vdw 2.527 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.533 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.545 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.547 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.557 3.040 ... (remaining 187780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 o \ r (resid 867 through 868 and (name N or name CA or name C or name O or name CB ) \ ) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and ( \ name N or name CA or name C or name O or name CB )) or resid 1147 through 1309)) \ selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 483 or resid 485 through 567 or (resid 568 and (name N \ or name CA or name C or name O or name CB )) or resid 569 through 582 or (resid \ 583 and (name N or name CA or name C or name O or name CB )) or resid 584 throug \ h 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or \ resid 587 through 618 or (resid 619 and (name N or name CA or name C or name O o \ r name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 through 747 o \ r (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 49 through 810 or (resid 811 and (name N or name CA or name C or name O or name \ CB )) or resid 813 or (resid 814 and (name N or name CA or name C or name O or n \ ame CB )) or resid 815 through 827 or resid 855 through 866 or (resid 867 throug \ h 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or name CA o \ r name C or name O or name CB )) or resid 1147 through 1309)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 483 or resid 485 through 527 or (resid 528 and (name N or name C \ A or name C or name O or name CB )) or resid 529 through 567 or (resid 568 and ( \ name N or name CA or name C or name O or name CB )) or resid 569 through 582 or \ (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 584 \ through 585 or (resid 586 and (name N or name CA or name C or name O or name CB \ )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C or n \ ame O or name CB )) or resid 620 through 813 or (resid 814 and (name N or name C \ A or name C or name O or name CB )) or resid 815 through 1091 or (resid 1092 and \ (name N or name CA or name C or name O or name CB )) or resid 1093 through 1141 \ or (resid 1142 and (name N or name CA or name C or name O or name CB )) or resi \ d 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1147 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.660 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.014 0.077 24359 Z= 0.787 Angle : 1.810 15.653 33251 Z= 1.198 Chirality : 0.102 1.405 3933 Planarity : 0.013 0.193 4191 Dihedral : 12.666 89.506 8334 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.06 % Favored : 94.60 % Rotamer: Outliers : 0.90 % Allowed : 2.24 % Favored : 96.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 2924 helix: -1.28 (0.16), residues: 677 sheet: 0.92 (0.21), residues: 547 loop : -0.68 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.172 0.020 TYR B 495 PHE 0.070 0.011 PHE B 718 TRP 0.198 0.023 TRP C 886 HIS 0.017 0.003 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01367 / 0.79 (24273) covalent geometry : angle 1.78272 / 1.20 (33031) SS BOND : bond 0.01717 / 1.03 ( 38) SS BOND : angle 1.95020 / 1.30 ( 76) hydrogen bonds : bond 0.16996 / 11.07 ( 1020) hydrogen bonds : angle 8.64365 / 5.92 ( 2844) link_BETA1-4 : bond 0.03063 / 1.95 ( 9) link_BETA1-4 : angle 6.56219 / 4.30 ( 27) link_NAG-ASN : bond 0.01357 / 0.84 ( 39) link_NAG-ASN : angle 4.62604 / 3.24 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 389 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.7975 (m110) cc_final: 0.7571 (p0) REVERT: A 358 ILE cc_start: 0.7812 (mm) cc_final: 0.7169 (mt) REVERT: A 656 VAL cc_start: 0.9056 (t) cc_final: 0.8776 (m) REVERT: A 900 MET cc_start: 0.8772 (ttm) cc_final: 0.8447 (ttp) REVERT: B 128 ILE cc_start: 0.7891 (mt) cc_final: 0.7622 (mp) REVERT: B 200 TYR cc_start: 0.4972 (m-80) cc_final: 0.4396 (m-80) REVERT: B 284 THR cc_start: 0.8742 (m) cc_final: 0.8430 (p) REVERT: B 392 PHE cc_start: 0.5827 (m-80) cc_final: 0.5453 (m-80) REVERT: B 809 PRO cc_start: 0.7876 (Cg_endo) cc_final: 0.7562 (Cg_exo) REVERT: C 129 LYS cc_start: 0.7821 (mttt) cc_final: 0.7193 (tttp) REVERT: C 305 SER cc_start: 0.9110 (t) cc_final: 0.8765 (p) REVERT: C 619 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: C 900 MET cc_start: 0.8326 (mtp) cc_final: 0.7984 (mtp) outliers start: 23 outliers final: 9 residues processed: 411 average time/residue: 0.1529 time to fit residues: 97.2607 Evaluate side-chains 209 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 619 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 856 ASN A1048 HIS A1119 ASN B 334 ASN B 540 ASN B 606 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 907 ASN B 955 ASN B1088 HIS C 271 GLN C 658 ASN C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133098 restraints weight = 30883.163| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.83 r_work: 0.3214 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24359 Z= 0.156 Angle : 0.714 13.482 33251 Z= 0.359 Chirality : 0.048 0.291 3933 Planarity : 0.004 0.051 4191 Dihedral : 6.121 72.269 3195 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 1.45 % Allowed : 7.07 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2924 helix: 1.03 (0.21), residues: 669 sheet: 0.71 (0.19), residues: 690 loop : -0.54 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 403 TYR 0.035 0.002 TYR C 396 PHE 0.031 0.002 PHE A 58 TRP 0.016 0.002 TRP B 353 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (24273) covalent geometry : angle 0.66541 / 0.35 (33031) SS BOND : bond 0.00389 / 0.26 ( 38) SS BOND : angle 1.83761 / 1.08 ( 76) hydrogen bonds : bond 0.05090 / 3.27 ( 1020) hydrogen bonds : angle 6.36047 / 4.36 ( 2844) link_BETA1-4 : bond 0.01122 / 0.74 ( 9) link_BETA1-4 : angle 4.36357 / 2.68 ( 27) link_NAG-ASN : bond 0.00448 / 0.27 ( 39) link_NAG-ASN : angle 3.64146 / 2.46 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.6887 (ttm-80) cc_final: 0.6313 (ttm-80) REVERT: A 358 ILE cc_start: 0.7557 (mm) cc_final: 0.7171 (mt) REVERT: A 656 VAL cc_start: 0.9224 (t) cc_final: 0.9016 (m) REVERT: B 284 THR cc_start: 0.8877 (m) cc_final: 0.8592 (p) REVERT: B 334 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7587 (t0) REVERT: B 347 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6260 (t80) REVERT: B 809 PRO cc_start: 0.7930 (Cg_endo) cc_final: 0.7719 (Cg_exo) REVERT: B 868 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8065 (tt0) REVERT: C 129 LYS cc_start: 0.7934 (mttt) cc_final: 0.7411 (mtmt) REVERT: C 239 GLN cc_start: 0.7286 (tm-30) cc_final: 0.7053 (tm-30) REVERT: C 646 ARG cc_start: 0.8578 (tpm170) cc_final: 0.8375 (tpm170) outliers start: 37 outliers final: 19 residues processed: 244 average time/residue: 0.1464 time to fit residues: 57.4118 Evaluate side-chains 186 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 619 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 51 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 856 ASN B 334 ASN B 856 ASN B 960 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130645 restraints weight = 30839.371| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.73 r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24359 Z= 0.199 Angle : 0.671 13.921 33251 Z= 0.335 Chirality : 0.047 0.257 3933 Planarity : 0.004 0.058 4191 Dihedral : 5.584 68.375 3188 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 1.81 % Allowed : 8.49 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 2924 helix: 1.32 (0.21), residues: 664 sheet: 0.57 (0.18), residues: 715 loop : -0.58 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1107 TYR 0.048 0.002 TYR C 396 PHE 0.019 0.002 PHE B1121 TRP 0.013 0.002 TRP C 886 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (24273) covalent geometry : angle 0.62836 / 0.32 (33031) SS BOND : bond 0.00563 / 0.34 ( 38) SS BOND : angle 1.83864 / 1.11 ( 76) hydrogen bonds : bond 0.04951 / 3.20 ( 1020) hydrogen bonds : angle 6.03777 / 4.14 ( 2844) link_BETA1-4 : bond 0.00945 / 0.65 ( 9) link_BETA1-4 : angle 4.12285 / 2.57 ( 27) link_NAG-ASN : bond 0.00413 / 0.27 ( 39) link_NAG-ASN : angle 3.19558 / 2.14 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7483 (mm) cc_final: 0.7170 (mt) REVERT: B 226 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7823 (mp) REVERT: B 307 THR cc_start: 0.8794 (m) cc_final: 0.8585 (t) REVERT: B 809 PRO cc_start: 0.7880 (Cg_endo) cc_final: 0.7654 (Cg_exo) REVERT: B 868 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7560 (tt0) REVERT: C 102 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7381 (mmt90) REVERT: C 239 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6872 (tm-30) REVERT: C 327 VAL cc_start: 0.8647 (t) cc_final: 0.8413 (m) outliers start: 46 outliers final: 32 residues processed: 211 average time/residue: 0.1412 time to fit residues: 49.1506 Evaluate side-chains 189 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 231 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 260 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 856 ASN B 901 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130682 restraints weight = 30810.191| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.78 r_work: 0.3145 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24359 Z= 0.118 Angle : 0.586 13.282 33251 Z= 0.292 Chirality : 0.044 0.252 3933 Planarity : 0.004 0.077 4191 Dihedral : 5.220 70.964 3187 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 1.93 % Allowed : 9.35 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2924 helix: 1.61 (0.21), residues: 670 sheet: 0.53 (0.19), residues: 710 loop : -0.52 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.027 0.001 TYR C 396 PHE 0.027 0.001 PHE B 855 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (24273) covalent geometry : angle 0.54732 / 0.28 (33031) SS BOND : bond 0.00404 / 0.23 ( 38) SS BOND : angle 1.70790 / 1.01 ( 76) hydrogen bonds : bond 0.04116 / 2.66 ( 1020) hydrogen bonds : angle 5.72873 / 3.93 ( 2844) link_BETA1-4 : bond 0.00904 / 0.61 ( 9) link_BETA1-4 : angle 3.88085 / 2.41 ( 27) link_NAG-ASN : bond 0.00335 / 0.21 ( 39) link_NAG-ASN : angle 2.78617 / 1.86 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7685 (mm) cc_final: 0.7249 (mt) REVERT: A 776 LYS cc_start: 0.8883 (tttt) cc_final: 0.8597 (ttmt) REVERT: A 935 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 307 THR cc_start: 0.8869 (m) cc_final: 0.8647 (t) REVERT: B 809 PRO cc_start: 0.7869 (Cg_endo) cc_final: 0.7659 (Cg_exo) REVERT: B 868 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7508 (tt0) REVERT: B 1107 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7371 (mtm110) REVERT: C 239 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6861 (tm-30) REVERT: C 511 VAL cc_start: 0.9044 (t) cc_final: 0.8833 (p) REVERT: C 780 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7913 (mm-30) REVERT: C 1142 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8002 (mm-40) outliers start: 49 outliers final: 29 residues processed: 221 average time/residue: 0.1438 time to fit residues: 52.2554 Evaluate side-chains 194 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 98 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 243 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 99 ASN C 207 HIS C 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131337 restraints weight = 30458.797| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.87 r_work: 0.3143 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24359 Z= 0.112 Angle : 0.565 13.026 33251 Z= 0.281 Chirality : 0.044 0.255 3933 Planarity : 0.003 0.053 4191 Dihedral : 5.021 71.339 3186 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 9.59 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.43 (0.15), residues: 2924 helix: 1.85 (0.21), residues: 663 sheet: 0.50 (0.19), residues: 706 loop : -0.48 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.020 0.001 TYR C 396 PHE 0.025 0.001 PHE B 855 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24273) covalent geometry : angle 0.52735 / 0.27 (33031) SS BOND : bond 0.00406 / 0.26 ( 38) SS BOND : angle 1.88006 / 1.13 ( 76) hydrogen bonds : bond 0.03896 / 2.52 ( 1020) hydrogen bonds : angle 5.56924 / 3.81 ( 2844) link_BETA1-4 : bond 0.00951 / 0.65 ( 9) link_BETA1-4 : angle 3.73247 / 2.33 ( 27) link_NAG-ASN : bond 0.00327 / 0.20 ( 39) link_NAG-ASN : angle 2.60535 / 1.73 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 307 THR cc_start: 0.8873 (m) cc_final: 0.8625 (t) REVERT: B 392 PHE cc_start: 0.6490 (m-80) cc_final: 0.6192 (m-80) REVERT: B 868 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7499 (tt0) REVERT: B 988 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: B 1107 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7400 (mtm110) REVERT: C 129 LYS cc_start: 0.7929 (mttt) cc_final: 0.7710 (mtmt) REVERT: C 239 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6870 (tm-30) REVERT: C 511 VAL cc_start: 0.9053 (t) cc_final: 0.8848 (p) REVERT: C 1142 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8016 (mm-40) outliers start: 49 outliers final: 36 residues processed: 217 average time/residue: 0.1556 time to fit residues: 54.3581 Evaluate side-chains 200 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 0.0670 chunk 275 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 189 optimal weight: 0.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 354 ASN B 856 ASN C 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131586 restraints weight = 30749.685| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.85 r_work: 0.3146 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24359 Z= 0.111 Angle : 0.550 12.872 33251 Z= 0.273 Chirality : 0.044 0.257 3933 Planarity : 0.003 0.049 4191 Dihedral : 4.891 71.386 3186 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 1.85 % Allowed : 9.90 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2924 helix: 2.02 (0.21), residues: 656 sheet: 0.55 (0.19), residues: 698 loop : -0.45 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.026 0.001 TYR A 508 PHE 0.018 0.001 PHE B 855 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24273) covalent geometry : angle 0.51335 / 0.26 (33031) SS BOND : bond 0.00424 / 0.24 ( 38) SS BOND : angle 1.80466 / 1.08 ( 76) hydrogen bonds : bond 0.03777 / 2.44 ( 1020) hydrogen bonds : angle 5.48104 / 3.75 ( 2844) link_BETA1-4 : bond 0.00918 / 0.62 ( 9) link_BETA1-4 : angle 3.61332 / 2.26 ( 27) link_NAG-ASN : bond 0.00331 / 0.20 ( 39) link_NAG-ASN : angle 2.51713 / 1.65 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 868 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7593 (tt0) REVERT: B 988 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: B 1107 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7364 (mtm110) REVERT: C 129 LYS cc_start: 0.7974 (mttt) cc_final: 0.7748 (mtmt) REVERT: C 239 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6901 (tm-30) REVERT: C 511 VAL cc_start: 0.9048 (t) cc_final: 0.8836 (p) REVERT: C 1142 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8071 (mm-40) outliers start: 47 outliers final: 34 residues processed: 215 average time/residue: 0.1533 time to fit residues: 53.0804 Evaluate side-chains 193 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 145 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 394 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 370 ASN B1002 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129821 restraints weight = 30744.798| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.70 r_work: 0.3118 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24359 Z= 0.232 Angle : 0.637 13.582 33251 Z= 0.317 Chirality : 0.047 0.263 3933 Planarity : 0.004 0.048 4191 Dihedral : 5.098 66.748 3186 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 2.16 % Allowed : 10.61 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2924 helix: 1.72 (0.21), residues: 656 sheet: 0.49 (0.19), residues: 697 loop : -0.57 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.022 0.002 TYR C 396 PHE 0.023 0.002 PHE B1121 TRP 0.013 0.002 TRP C 886 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.23 (24273) covalent geometry : angle 0.60000 / 0.31 (33031) SS BOND : bond 0.00539 / 0.31 ( 38) SS BOND : angle 2.39537 / 1.46 ( 76) hydrogen bonds : bond 0.04721 / 3.06 ( 1020) hydrogen bonds : angle 5.69960 / 3.90 ( 2844) link_BETA1-4 : bond 0.00892 / 0.60 ( 9) link_BETA1-4 : angle 3.61136 / 2.29 ( 27) link_NAG-ASN : bond 0.00338 / 0.22 ( 39) link_NAG-ASN : angle 2.64887 / 1.76 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8419 (tt0) REVERT: B 307 THR cc_start: 0.9066 (m) cc_final: 0.8765 (t) REVERT: B 868 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7836 (tt0) REVERT: B 916 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8801 (tp) REVERT: B 1107 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7907 (mtm-85) REVERT: C 129 LYS cc_start: 0.8192 (mttt) cc_final: 0.7893 (mttt) REVERT: C 564 GLN cc_start: 0.7154 (tp40) cc_final: 0.6930 (tt0) outliers start: 55 outliers final: 43 residues processed: 203 average time/residue: 0.1410 time to fit residues: 46.6115 Evaluate side-chains 198 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129959 restraints weight = 30707.104| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.87 r_work: 0.3153 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24359 Z= 0.133 Angle : 0.570 13.139 33251 Z= 0.283 Chirality : 0.044 0.257 3933 Planarity : 0.003 0.049 4191 Dihedral : 4.881 69.515 3186 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.73 % Allowed : 11.00 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 2924 helix: 1.85 (0.21), residues: 668 sheet: 0.52 (0.19), residues: 693 loop : -0.51 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.020 0.001 TYR C 396 PHE 0.022 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (24273) covalent geometry : angle 0.53340 / 0.27 (33031) SS BOND : bond 0.00387 / 0.23 ( 38) SS BOND : angle 2.15111 / 1.29 ( 76) hydrogen bonds : bond 0.04030 / 2.61 ( 1020) hydrogen bonds : angle 5.53116 / 3.78 ( 2844) link_BETA1-4 : bond 0.00852 / 0.60 ( 9) link_BETA1-4 : angle 3.54017 / 2.23 ( 27) link_NAG-ASN : bond 0.00292 / 0.18 ( 39) link_NAG-ASN : angle 2.46965 / 1.62 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8304 (tt0) REVERT: B 854 LYS cc_start: 0.7276 (tptp) cc_final: 0.6440 (tptm) REVERT: B 868 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7537 (tt0) REVERT: B 988 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 1107 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7620 (mtm-85) REVERT: C 129 LYS cc_start: 0.8120 (mttt) cc_final: 0.7890 (mttt) REVERT: C 239 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6853 (tm-30) outliers start: 44 outliers final: 33 residues processed: 194 average time/residue: 0.1556 time to fit residues: 49.0498 Evaluate side-chains 189 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 264 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 290 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 99 ASN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.167562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130834 restraints weight = 30716.538| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24359 Z= 0.114 Angle : 0.549 12.870 33251 Z= 0.272 Chirality : 0.043 0.257 3933 Planarity : 0.003 0.050 4191 Dihedral : 4.729 69.772 3186 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.53 % Allowed : 11.36 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2924 helix: 2.03 (0.21), residues: 665 sheet: 0.48 (0.19), residues: 692 loop : -0.48 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.021 0.001 TYR C 396 PHE 0.022 0.001 PHE B 855 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (24273) covalent geometry : angle 0.51469 / 0.26 (33031) SS BOND : bond 0.00365 / 0.22 ( 38) SS BOND : angle 1.94321 / 1.16 ( 76) hydrogen bonds : bond 0.03772 / 2.44 ( 1020) hydrogen bonds : angle 5.40445 / 3.70 ( 2844) link_BETA1-4 : bond 0.00932 / 0.63 ( 9) link_BETA1-4 : angle 3.45026 / 2.16 ( 27) link_NAG-ASN : bond 0.00294 / 0.18 ( 39) link_NAG-ASN : angle 2.36123 / 1.55 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7722 (mm) cc_final: 0.7286 (mt) REVERT: B 854 LYS cc_start: 0.7262 (tptp) cc_final: 0.6420 (tptm) REVERT: B 868 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7470 (tt0) REVERT: B 988 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: C 239 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6845 (tm-30) outliers start: 39 outliers final: 33 residues processed: 194 average time/residue: 0.1571 time to fit residues: 49.7119 Evaluate side-chains 189 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131076 restraints weight = 30763.611| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.82 r_work: 0.3167 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24359 Z= 0.117 Angle : 0.546 12.782 33251 Z= 0.271 Chirality : 0.043 0.259 3933 Planarity : 0.003 0.050 4191 Dihedral : 4.662 69.805 3186 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.57 % Allowed : 11.59 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2924 helix: 2.09 (0.21), residues: 664 sheet: 0.47 (0.19), residues: 698 loop : -0.46 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 403 TYR 0.026 0.001 TYR C 396 PHE 0.024 0.001 PHE B 855 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (24273) covalent geometry : angle 0.51400 / 0.26 (33031) SS BOND : bond 0.00380 / 0.23 ( 38) SS BOND : angle 1.83513 / 1.09 ( 76) hydrogen bonds : bond 0.03751 / 2.43 ( 1020) hydrogen bonds : angle 5.35855 / 3.67 ( 2844) link_BETA1-4 : bond 0.00894 / 0.60 ( 9) link_BETA1-4 : angle 3.37034 / 2.10 ( 27) link_NAG-ASN : bond 0.00296 / 0.18 ( 39) link_NAG-ASN : angle 2.31399 / 1.51 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7750 (mm) cc_final: 0.7328 (mt) REVERT: B 854 LYS cc_start: 0.7264 (tptp) cc_final: 0.6417 (tptm) REVERT: B 868 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7481 (tt0) REVERT: B 988 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: C 360 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7740 (m-40) REVERT: C 794 ILE cc_start: 0.7602 (pt) cc_final: 0.7391 (mm) outliers start: 40 outliers final: 33 residues processed: 196 average time/residue: 0.1549 time to fit residues: 49.3946 Evaluate side-chains 193 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 196 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130848 restraints weight = 30535.153| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.85 r_work: 0.3159 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24359 Z= 0.119 Angle : 0.561 12.915 33251 Z= 0.278 Chirality : 0.044 0.259 3933 Planarity : 0.003 0.050 4191 Dihedral : 4.648 69.686 3186 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 2924 helix: 2.08 (0.21), residues: 667 sheet: 0.47 (0.19), residues: 700 loop : -0.44 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.028 0.001 TYR C 396 PHE 0.020 0.001 PHE C 168 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (24273) covalent geometry : angle 0.52288 / 0.27 (33031) SS BOND : bond 0.00372 / 0.23 ( 38) SS BOND : angle 2.56573 / 1.52 ( 76) hydrogen bonds : bond 0.03729 / 2.41 ( 1020) hydrogen bonds : angle 5.34674 / 3.66 ( 2844) link_BETA1-4 : bond 0.00902 / 0.61 ( 9) link_BETA1-4 : angle 3.35432 / 2.11 ( 27) link_NAG-ASN : bond 0.00291 / 0.18 ( 39) link_NAG-ASN : angle 2.28602 / 1.49 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4789.54 seconds wall clock time: 83 minutes 5.95 seconds (4985.95 seconds total)