Starting phenix.real_space_refine on Sun Jul 5 10:17:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhy_34807/07_2026/8hhy_34807.cif" } resolution = 2.77 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= 0.001 sd= 0.077 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 123 5.16 5 C 17431 2.51 5 N 4528 2.21 5 O 5338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 27420 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "W" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 675 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 753 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 819 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 660 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 86} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 7454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7454 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 45, 'TRANS': 911} Chain breaks: 10 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7574 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 924} Chain breaks: 9 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 7264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7264 Classifications: {'peptide': 934} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 44, 'TRANS': 889} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.69, per 1000 atoms: 0.21 Number of scatterers: 27420 At special positions: 0 Unit cell: (157.7, 158.53, 182.6, 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 123 16.00 O 5338 8.00 N 4528 7.00 C 17431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 717 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 717 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 801 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 62 sheets defined 22.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'W' and resid 79 through 83 removed outlier: 4.079A pdb=" N ILE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.872A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.045A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.847A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.644A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.593A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.003A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.024A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.873A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 759 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.115A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) 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 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: 3.552A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.830A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.672A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.595A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.807A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.926A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 940 removed outlier: 4.267A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (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 977 through 984 removed outlier: 3.508A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.564A pdb=" N TRP F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.602A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR F 80 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN F 82 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'W' and resid 48 through 49 removed outlier: 3.947A pdb=" N TYR W 49 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN W 53 " --> pdb=" O TYR W 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'W' and resid 66 through 67 removed outlier: 3.748A pdb=" N SER W 67 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'W' and resid 89 through 91 removed outlier: 4.651A pdb=" N GLN W 90 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR W 97 " --> pdb=" O GLN W 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.995A pdb=" N TRP G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY G 99 " --> pdb=" O TRP G 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AA8, first strand: chain 'G' and resid 49 through 52 removed outlier: 3.738A pdb=" N ARG G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 57 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 68 through 73 removed outlier: 4.151A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 36 through 37 removed outlier: 4.424A pdb=" N GLN I 37 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 48 through 49 removed outlier: 4.168A pdb=" N TYR I 49 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 90 through 91 removed outlier: 4.604A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.538A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.675A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.530A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AC4, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.777A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.384A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.614A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.673A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.550A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.914A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.549A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AD5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.701A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.344A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.950A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.287A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.901A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.756A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.552A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 52 removed outlier: 7.878A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AF4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF5, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AF6, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AF7, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.723A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AF9, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.605A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AG2, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.981A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.115A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.365A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG6, first strand: chain 'C' and resid 718 through 727 Processing sheet with id=AG7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 3.699A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C1103 " --> pdb=" O VAL C1096 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2358 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: 6.28 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8766 1.35 - 1.47: 7212 1.47 - 1.60: 11871 1.60 - 1.73: 1 1.73 - 1.85: 159 Bond restraints: 28009 Sorted by residual: bond pdb=" CG PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 1.503 1.367 0.136 3.40e-02 8.65e+02 1.60e+01 bond pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" CB PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C MET H 40 " pdb=" N PRO H 41 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.66e+00 ... (remaining 28004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 37782 2.88 - 5.76: 266 5.76 - 8.64: 28 8.64 - 11.52: 6 11.52 - 14.40: 2 Bond angle restraints: 38084 Sorted by residual: angle pdb=" N PRO B 272 " pdb=" CD PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 103.20 92.64 10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 112.00 102.66 9.34 1.40e+00 5.10e-01 4.45e+01 angle pdb=" CG1 ILE L 29 " pdb=" CB ILE L 29 " pdb=" CG2 ILE L 29 " ideal model delta sigma weight residual 110.70 125.10 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C ILE L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" N PRO C1090 " pdb=" CD PRO C1090 " pdb=" CG PRO C1090 " ideal model delta sigma weight residual 103.20 96.50 6.70 1.50e+00 4.44e-01 1.99e+01 ... (remaining 38079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14942 17.89 - 35.77: 1185 35.77 - 53.66: 178 53.66 - 71.54: 55 71.54 - 89.43: 43 Dihedral angle restraints: 16403 sinusoidal: 6306 harmonic: 10097 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 16400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4402 0.148 - 0.295: 18 0.295 - 0.443: 0 0.443 - 0.591: 0 0.591 - 0.738: 2 Chirality restraints: 4422 Sorted by residual: chirality pdb=" CB ILE L 29 " pdb=" CA ILE L 29 " pdb=" CG1 ILE L 29 " pdb=" CG2 ILE L 29 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4419 not shown) Planarity restraints: 4900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.000 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN B 616 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 9 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ALA H 9 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA H 9 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU H 10 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.063 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO C1079 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.051 5.00e-02 4.00e+02 ... (remaining 4897 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 386 2.64 - 3.20: 24988 3.20 - 3.77: 41071 3.77 - 4.33: 57633 4.33 - 4.90: 92203 Nonbonded interactions: 216281 Sorted by model distance: nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.074 3.040 nonbonded pdb=" OE2 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.082 3.040 nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.111 3.040 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.128 3.040 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.129 3.120 ... (remaining 216276 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 141 or (resid 142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 442 or resid 502 through 1120 o \ r (resid 1121 and (name N or name CA or name C or name O or name CB )) or resid \ 1122 through 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 68 or resid 80 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or resi \ d 166 through 209 or resid 216 through 243 or resid 263 through 442 or resid 502 \ through 1308)) selection = (chain 'C' and (resid 27 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 209 or resid 216 t \ hrough 1120 or (resid 1121 and (name N or name CA or name C or name O or name CB \ )) or resid 1122 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 3 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 15 or (resid 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 or (re \ sid 27 through 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 31 or (resid 32 through 33 and (name N or name CA or name C or na \ me O or name CB )) or resid 34 through 54 or (resid 55 through 60 and (name N or \ name CA or name C or name O or name CB )) or resid 61 through 64 or (resid 65 a \ nd (name N or name CA or name C or name O or name CB )) or resid 66 through 72 o \ r (resid 73 through 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 99 or (resid 100 through 106 and (name N or name CA or name \ C or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA or n \ ame C or name O or name CB )) or resid 109 through 120)) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'L' and (resid 2 through 8 or resid 15 through 92)) selection = (chain 'W' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) } 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.900 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 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 : 0.004 0.147 28083 Z= 0.189 Angle : 0.732 17.070 38264 Z= 0.380 Chirality : 0.049 0.738 4422 Planarity : 0.005 0.096 4872 Dihedral : 13.812 89.431 9781 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.14), residues: 3407 helix: -0.80 (0.19), residues: 653 sheet: -1.22 (0.21), residues: 655 loop : -1.47 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 905 TYR 0.022 0.001 TYR A 873 PHE 0.035 0.001 PHE C 906 TRP 0.024 0.001 TRP C 886 HIS 0.021 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (28009) covalent geometry : angle 0.69377 / 0.37 (38084) SS BOND : bond 0.00243 / 0.18 ( 42) SS BOND : angle 2.30302 / 1.38 ( 84) hydrogen bonds : bond 0.20824 / 13.94 ( 855) hydrogen bonds : angle 9.60943 / 6.53 ( 2358) link_BETA1-4 : bond 0.00379 / 0.19 ( 4) link_BETA1-4 : angle 0.86019 / 0.55 ( 12) link_NAG-ASN : bond 0.00701 / 0.45 ( 28) link_NAG-ASN : angle 4.53390 / 3.18 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.0484 (mtm) cc_final: 0.0270 (tmt) REVERT: A 902 MET cc_start: 0.5852 (tpt) cc_final: 0.5516 (mmm) REVERT: C 912 THR cc_start: 0.5915 (t) cc_final: 0.5590 (m) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.5028 time to fit residues: 156.4121 Evaluate side-chains 168 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.0370 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 34 ASN W 89 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 271 GLN B 501 ASN B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 314 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.270750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.243652 restraints weight = 36908.131| |-----------------------------------------------------------------------------| r_work (start): 0.4849 rms_B_bonded: 1.91 r_work: 0.4567 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28083 Z= 0.159 Angle : 0.651 13.713 38264 Z= 0.333 Chirality : 0.046 0.286 4422 Planarity : 0.005 0.065 4872 Dihedral : 5.017 32.513 3716 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 1.34 % Allowed : 7.38 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3407 helix: -0.44 (0.20), residues: 661 sheet: -1.20 (0.20), residues: 674 loop : -1.44 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.023 0.001 TYR C1067 PHE 0.026 0.001 PHE C 906 TRP 0.021 0.001 TRP C 886 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (28009) covalent geometry : angle 0.62515 / 0.33 (38084) SS BOND : bond 0.00295 / 0.21 ( 42) SS BOND : angle 1.73961 / 1.13 ( 84) hydrogen bonds : bond 0.05911 / 4.00 ( 855) hydrogen bonds : angle 7.52158 / 5.16 ( 2358) link_BETA1-4 : bond 0.00237 / 0.12 ( 4) link_BETA1-4 : angle 0.91018 / 0.57 ( 12) link_NAG-ASN : bond 0.00588 / 0.39 ( 28) link_NAG-ASN : angle 3.55459 / 2.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0140 (ptt) cc_final: -0.1737 (mpt) REVERT: G 40 MET cc_start: 0.2026 (pmm) cc_final: 0.0909 (ptt) REVERT: L 4 MET cc_start: 0.0698 (mtm) cc_final: 0.0152 (tmt) REVERT: A 1001 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7636 (tt) REVERT: B 1001 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (tt) outliers start: 40 outliers final: 16 residues processed: 223 average time/residue: 0.4715 time to fit residues: 130.1617 Evaluate side-chains 186 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 273 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 218 optimal weight: 0.0980 chunk 336 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.270372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.242611 restraints weight = 36901.258| |-----------------------------------------------------------------------------| r_work (start): 0.4828 rms_B_bonded: 1.97 r_work: 0.4557 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28083 Z= 0.145 Angle : 0.613 12.265 38264 Z= 0.311 Chirality : 0.045 0.256 4422 Planarity : 0.004 0.067 4872 Dihedral : 4.821 29.330 3716 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.15 % Allowed : 10.20 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3407 helix: -0.12 (0.20), residues: 657 sheet: -1.09 (0.20), residues: 673 loop : -1.42 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.019 0.001 TYR B 369 PHE 0.032 0.001 PHE B 168 TRP 0.017 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (28009) covalent geometry : angle 0.59007 / 0.31 (38084) SS BOND : bond 0.00279 / 0.20 ( 42) SS BOND : angle 1.47608 / 0.99 ( 84) hydrogen bonds : bond 0.05465 / 3.70 ( 855) hydrogen bonds : angle 7.00063 / 4.80 ( 2358) link_BETA1-4 : bond 0.00355 / 0.18 ( 4) link_BETA1-4 : angle 0.88476 / 0.56 ( 12) link_NAG-ASN : bond 0.00622 / 0.38 ( 28) link_NAG-ASN : angle 3.33220 / 2.30 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 MET cc_start: 0.4624 (OUTLIER) cc_final: 0.2939 (pmm) REVERT: W 4 MET cc_start: -0.0105 (ptt) cc_final: -0.1710 (mpt) REVERT: G 40 MET cc_start: 0.1977 (pmm) cc_final: 0.0975 (ptt) REVERT: A 740 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5146 (mtp) REVERT: A 900 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7886 (mtt) REVERT: A 1001 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7550 (tt) REVERT: B 275 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5872 (t80) REVERT: B 1001 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 926 GLN cc_start: 0.5892 (tm130) cc_final: 0.5625 (tm130) outliers start: 64 outliers final: 23 residues processed: 240 average time/residue: 0.4476 time to fit residues: 135.1413 Evaluate side-chains 189 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 33 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 23 optimal weight: 30.0000 chunk 293 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 12 optimal weight: 0.0070 chunk 10 optimal weight: 40.0000 chunk 159 optimal weight: 5.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 6 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 762 GLN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.267987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.241942 restraints weight = 36327.264| |-----------------------------------------------------------------------------| r_work (start): 0.4828 rms_B_bonded: 1.73 r_work: 0.4534 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28083 Z= 0.205 Angle : 0.668 11.076 38264 Z= 0.339 Chirality : 0.046 0.253 4422 Planarity : 0.005 0.065 4872 Dihedral : 5.033 28.610 3716 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 2.72 % Allowed : 12.21 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3407 helix: -0.21 (0.20), residues: 657 sheet: -1.20 (0.20), residues: 669 loop : -1.43 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1091 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE B 168 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (28009) covalent geometry : angle 0.64742 / 0.33 (38084) SS BOND : bond 0.00288 / 0.21 ( 42) SS BOND : angle 1.52137 / 1.07 ( 84) hydrogen bonds : bond 0.05886 / 4.00 ( 855) hydrogen bonds : angle 7.03490 / 4.80 ( 2358) link_BETA1-4 : bond 0.00348 / 0.17 ( 4) link_BETA1-4 : angle 1.09170 / 0.67 ( 12) link_NAG-ASN : bond 0.00519 / 0.34 ( 28) link_NAG-ASN : angle 3.31882 / 2.30 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0135 (ptt) cc_final: -0.1685 (mpt) REVERT: L 4 MET cc_start: -0.0192 (mmm) cc_final: -0.1039 (tmt) REVERT: A 567 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.5616 (mpp80) REVERT: A 740 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5190 (mtp) REVERT: A 984 LEU cc_start: 0.3201 (OUTLIER) cc_final: 0.2127 (mp) REVERT: A 1001 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 1001 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7989 (tt) REVERT: B 1091 ARG cc_start: 0.7429 (mmt-90) cc_final: 0.5989 (mpp-170) REVERT: B 1106 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7403 (pt0) outliers start: 81 outliers final: 38 residues processed: 240 average time/residue: 0.4142 time to fit residues: 125.1102 Evaluate side-chains 204 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 219 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 159 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 289 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.266959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.241454 restraints weight = 36338.833| |-----------------------------------------------------------------------------| r_work (start): 0.4823 rms_B_bonded: 1.69 r_work: 0.4539 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28083 Z= 0.218 Angle : 0.687 15.722 38264 Z= 0.346 Chirality : 0.047 0.256 4422 Planarity : 0.004 0.065 4872 Dihedral : 5.133 27.701 3716 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.57 % Rotamer: Outliers : 3.09 % Allowed : 13.32 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3407 helix: -0.33 (0.20), residues: 656 sheet: -1.34 (0.20), residues: 665 loop : -1.45 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1091 TYR 0.024 0.002 TYR C1067 PHE 0.028 0.002 PHE C 927 TRP 0.017 0.001 TRP C 886 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (28009) covalent geometry : angle 0.66567 / 0.34 (38084) SS BOND : bond 0.00295 / 0.22 ( 42) SS BOND : angle 1.64818 / 1.12 ( 84) hydrogen bonds : bond 0.06039 / 4.11 ( 855) hydrogen bonds : angle 7.01255 / 4.79 ( 2358) link_BETA1-4 : bond 0.00306 / 0.15 ( 4) link_BETA1-4 : angle 1.13583 / 0.69 ( 12) link_NAG-ASN : bond 0.00521 / 0.34 ( 28) link_NAG-ASN : angle 3.30711 / 2.30 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 180 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0109 (ptt) cc_final: -0.1642 (mpt) REVERT: G 40 MET cc_start: 0.2040 (pmm) cc_final: 0.0805 (ptt) REVERT: H 93 MET cc_start: 0.0552 (mtt) cc_final: -0.1715 (tmm) REVERT: L 4 MET cc_start: -0.0036 (mmm) cc_final: -0.0928 (tmt) REVERT: A 34 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5610 (mpt180) REVERT: A 567 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.5678 (mpp80) REVERT: A 740 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5065 (mtp) REVERT: A 878 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 984 LEU cc_start: 0.3047 (OUTLIER) cc_final: 0.1976 (mp) REVERT: A 1001 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 1106 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: C 926 GLN cc_start: 0.6182 (tm130) cc_final: 0.5870 (tm130) outliers start: 92 outliers final: 40 residues processed: 250 average time/residue: 0.4675 time to fit residues: 146.1556 Evaluate side-chains 204 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 160 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 342 optimal weight: 0.0000 chunk 207 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.266354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.237661 restraints weight = 36167.670| |-----------------------------------------------------------------------------| r_work (start): 0.4792 rms_B_bonded: 1.81 r_work: 0.4505 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28083 Z= 0.225 Angle : 0.695 11.320 38264 Z= 0.351 Chirality : 0.047 0.258 4422 Planarity : 0.004 0.062 4872 Dihedral : 5.207 29.450 3716 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 3.42 % Allowed : 14.43 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3407 helix: -0.43 (0.19), residues: 659 sheet: -1.37 (0.20), residues: 658 loop : -1.46 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1091 TYR 0.025 0.002 TYR C1067 PHE 0.031 0.002 PHE C 927 TRP 0.015 0.001 TRP C 886 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (28009) covalent geometry : angle 0.67343 / 0.35 (38084) SS BOND : bond 0.00327 / 0.25 ( 42) SS BOND : angle 1.84106 / 1.29 ( 84) hydrogen bonds : bond 0.06123 / 4.17 ( 855) hydrogen bonds : angle 7.02929 / 4.80 ( 2358) link_BETA1-4 : bond 0.00322 / 0.16 ( 4) link_BETA1-4 : angle 1.15765 / 0.70 ( 12) link_NAG-ASN : bond 0.00530 / 0.34 ( 28) link_NAG-ASN : angle 3.31889 / 2.31 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 175 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0102 (ptt) cc_final: -0.1591 (mpt) REVERT: H 93 MET cc_start: 0.0629 (mtt) cc_final: -0.1560 (tmm) REVERT: L 4 MET cc_start: -0.0111 (mmm) cc_final: -0.0992 (tmt) REVERT: A 567 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.5732 (mpp80) REVERT: A 740 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5047 (mtp) REVERT: A 811 LYS cc_start: 0.4304 (tmtt) cc_final: 0.3930 (ttpt) REVERT: A 878 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7201 (tt) REVERT: A 984 LEU cc_start: 0.3058 (OUTLIER) cc_final: 0.1930 (mp) REVERT: A 1001 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 858 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6140 (pt) REVERT: B 978 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6746 (t0) REVERT: C 811 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5817 (mppt) REVERT: C 865 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6387 (mp) outliers start: 102 outliers final: 46 residues processed: 254 average time/residue: 0.4605 time to fit residues: 146.1216 Evaluate side-chains 219 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 0.0270 chunk 131 optimal weight: 0.0370 chunk 232 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 314 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1023 ASN A1058 HIS A1113 GLN B 196 ASN B 317 ASN B 675 GLN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.269255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.241887 restraints weight = 36613.219| |-----------------------------------------------------------------------------| r_work (start): 0.4824 rms_B_bonded: 1.89 r_work: 0.4596 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28083 Z= 0.137 Angle : 0.631 23.989 38264 Z= 0.313 Chirality : 0.046 0.739 4422 Planarity : 0.004 0.068 4872 Dihedral : 4.830 27.777 3716 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.58 % Allowed : 15.54 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3407 helix: -0.13 (0.20), residues: 658 sheet: -1.24 (0.20), residues: 644 loop : -1.37 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.019 0.001 TYR B 369 PHE 0.022 0.001 PHE C 927 TRP 0.015 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (28009) covalent geometry : angle 0.59624 / 0.30 (38084) SS BOND : bond 0.00257 / 0.19 ( 42) SS BOND : angle 1.51175 / 1.05 ( 84) hydrogen bonds : bond 0.05332 / 3.63 ( 855) hydrogen bonds : angle 6.62804 / 4.54 ( 2358) link_BETA1-4 : bond 0.00339 / 0.17 ( 4) link_BETA1-4 : angle 0.98259 / 0.61 ( 12) link_NAG-ASN : bond 0.00601 / 0.37 ( 28) link_NAG-ASN : angle 4.19104 / 3.07 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 183 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0147 (ptt) cc_final: -0.1603 (mpt) REVERT: G 40 MET cc_start: 0.2229 (pmm) cc_final: 0.0906 (ptt) REVERT: H 93 MET cc_start: 0.0380 (mtt) cc_final: -0.1671 (tmm) REVERT: L 4 MET cc_start: -0.0189 (mmm) cc_final: -0.0970 (tmt) REVERT: A 567 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.5727 (mpp80) REVERT: A 650 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6249 (tt) REVERT: A 740 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5617 (mtp) REVERT: A 878 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 984 LEU cc_start: 0.2973 (OUTLIER) cc_final: 0.2107 (mp) REVERT: A 1001 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7650 (tt) REVERT: B 650 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6761 (tt) outliers start: 77 outliers final: 39 residues processed: 244 average time/residue: 0.4184 time to fit residues: 130.1708 Evaluate side-chains 211 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 250 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 335 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 336 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.268379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.240775 restraints weight = 36674.568| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 1.89 r_work: 0.4586 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28083 Z= 0.159 Angle : 0.633 19.037 38264 Z= 0.316 Chirality : 0.045 0.499 4422 Planarity : 0.004 0.065 4872 Dihedral : 4.868 27.466 3716 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 2.62 % Allowed : 15.97 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3407 helix: -0.14 (0.20), residues: 661 sheet: -1.21 (0.20), residues: 643 loop : -1.34 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.025 0.001 TYR C1067 PHE 0.028 0.001 PHE C 927 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (28009) covalent geometry : angle 0.60456 / 0.31 (38084) SS BOND : bond 0.00263 / 0.19 ( 42) SS BOND : angle 1.65099 / 1.09 ( 84) hydrogen bonds : bond 0.05393 / 3.67 ( 855) hydrogen bonds : angle 6.59049 / 4.51 ( 2358) link_BETA1-4 : bond 0.00309 / 0.15 ( 4) link_BETA1-4 : angle 1.01096 / 0.64 ( 12) link_NAG-ASN : bond 0.00509 / 0.32 ( 28) link_NAG-ASN : angle 3.73527 / 2.71 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0161 (ptt) cc_final: -0.1599 (mpt) REVERT: G 40 MET cc_start: 0.2448 (pmm) cc_final: 0.1259 (ptp) REVERT: H 93 MET cc_start: 0.0428 (mtt) cc_final: -0.1632 (tmm) REVERT: L 4 MET cc_start: -0.0315 (mmm) cc_final: -0.1034 (tmt) REVERT: A 141 LEU cc_start: -0.0164 (OUTLIER) cc_final: -0.0669 (pp) REVERT: A 567 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.5660 (mpp80) REVERT: A 650 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6342 (tt) REVERT: A 709 ASN cc_start: 0.5677 (p0) cc_final: 0.5437 (p0) REVERT: A 740 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5683 (mtp) REVERT: A 878 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7112 (tt) REVERT: A 984 LEU cc_start: 0.3186 (OUTLIER) cc_final: 0.2213 (mp) REVERT: A 1001 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7661 (tt) REVERT: B 650 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6735 (tt) REVERT: B 1058 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5858 (m-70) outliers start: 78 outliers final: 46 residues processed: 240 average time/residue: 0.4264 time to fit residues: 130.2882 Evaluate side-chains 218 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 180 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 227 optimal weight: 0.6980 chunk 290 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 328 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 263 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 762 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.266710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.237944 restraints weight = 36369.702| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 1.95 r_work: 0.4506 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28083 Z= 0.204 Angle : 0.681 16.078 38264 Z= 0.342 Chirality : 0.047 0.500 4422 Planarity : 0.004 0.064 4872 Dihedral : 5.049 26.791 3716 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 2.62 % Allowed : 16.21 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3407 helix: -0.27 (0.20), residues: 656 sheet: -1.29 (0.20), residues: 653 loop : -1.35 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.029 0.002 TYR C1067 PHE 0.033 0.002 PHE C 718 TRP 0.012 0.001 TRP C 886 HIS 0.014 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (28009) covalent geometry : angle 0.65366 / 0.34 (38084) SS BOND : bond 0.00315 / 0.22 ( 42) SS BOND : angle 1.72912 / 1.12 ( 84) hydrogen bonds : bond 0.05797 / 3.95 ( 855) hydrogen bonds : angle 6.72854 / 4.59 ( 2358) link_BETA1-4 : bond 0.00311 / 0.16 ( 4) link_BETA1-4 : angle 1.08956 / 0.67 ( 12) link_NAG-ASN : bond 0.00498 / 0.32 ( 28) link_NAG-ASN : angle 3.78747 / 2.69 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0203 (ptt) cc_final: -0.1646 (mpt) REVERT: G 40 MET cc_start: 0.2579 (pmm) cc_final: 0.1290 (ptp) REVERT: G 93 MET cc_start: 0.1388 (pp-130) cc_final: 0.1051 (tmm) REVERT: H 93 MET cc_start: 0.0533 (mtt) cc_final: -0.1471 (tmm) REVERT: L 4 MET cc_start: -0.0185 (mmm) cc_final: -0.1031 (tmt) REVERT: A 567 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.5704 (mpp80) REVERT: A 650 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6410 (tt) REVERT: A 709 ASN cc_start: 0.5648 (p0) cc_final: 0.5438 (p0) REVERT: A 740 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5673 (mtp) REVERT: A 811 LYS cc_start: 0.4433 (tmtt) cc_final: 0.3957 (ttpm) REVERT: A 878 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7169 (tt) REVERT: A 900 MET cc_start: 0.8001 (mmt) cc_final: 0.7800 (mmt) REVERT: A 984 LEU cc_start: 0.3143 (OUTLIER) cc_final: 0.2028 (mp) REVERT: A 1001 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7773 (tt) REVERT: B 858 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6092 (pt) REVERT: C 926 GLN cc_start: 0.6149 (tm130) cc_final: 0.5791 (tm130) outliers start: 78 outliers final: 47 residues processed: 230 average time/residue: 0.4087 time to fit residues: 118.6990 Evaluate side-chains 220 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 328 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 278 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 762 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.267578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.238158 restraints weight = 36401.428| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 1.99 r_work: 0.4508 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28083 Z= 0.175 Angle : 0.656 15.310 38264 Z= 0.329 Chirality : 0.046 0.452 4422 Planarity : 0.004 0.064 4872 Dihedral : 4.978 27.213 3716 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.28 % Allowed : 16.71 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3407 helix: -0.25 (0.20), residues: 655 sheet: -1.29 (0.20), residues: 636 loop : -1.34 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.028 0.001 TYR C1067 PHE 0.029 0.002 PHE C 718 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (28009) covalent geometry : angle 0.62941 / 0.32 (38084) SS BOND : bond 0.00269 / 0.21 ( 42) SS BOND : angle 1.65199 / 1.08 ( 84) hydrogen bonds : bond 0.05613 / 3.83 ( 855) hydrogen bonds : angle 6.66459 / 4.54 ( 2358) link_BETA1-4 : bond 0.00301 / 0.15 ( 4) link_BETA1-4 : angle 1.03738 / 0.65 ( 12) link_NAG-ASN : bond 0.00491 / 0.31 ( 28) link_NAG-ASN : angle 3.63868 / 2.59 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0212 (ptt) cc_final: -0.1640 (mpt) REVERT: G 40 MET cc_start: 0.2596 (pmm) cc_final: 0.1296 (ptp) REVERT: H 93 MET cc_start: 0.0479 (mtt) cc_final: -0.1471 (tmm) REVERT: L 4 MET cc_start: -0.0106 (mmm) cc_final: -0.1004 (tmt) REVERT: A 567 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.5682 (mpp80) REVERT: A 650 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6388 (tt) REVERT: A 709 ASN cc_start: 0.5600 (p0) cc_final: 0.5375 (p0) REVERT: A 740 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5683 (mtp) REVERT: A 811 LYS cc_start: 0.4443 (tmtt) cc_final: 0.3971 (ttpm) REVERT: A 878 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7139 (tt) REVERT: A 984 LEU cc_start: 0.3321 (OUTLIER) cc_final: 0.2219 (mp) REVERT: A 1001 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 650 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6774 (tt) REVERT: B 858 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5932 (pt) REVERT: B 978 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6880 (t0) REVERT: B 1058 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.6282 (m170) REVERT: C 926 GLN cc_start: 0.6145 (tm130) cc_final: 0.5805 (tm130) outliers start: 68 outliers final: 48 residues processed: 226 average time/residue: 0.4094 time to fit residues: 117.9776 Evaluate side-chains 226 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 300 optimal weight: 4.9990 chunk 309 optimal weight: 0.6980 chunk 56 optimal weight: 50.0000 chunk 137 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 317 ASN B 762 GLN B 919 ASN B1010 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.264157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.235364 restraints weight = 36037.556| |-----------------------------------------------------------------------------| r_work (start): 0.4778 rms_B_bonded: 1.86 r_work: 0.4549 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 28083 Z= 0.320 Angle : 0.835 14.707 38264 Z= 0.421 Chirality : 0.051 0.453 4422 Planarity : 0.005 0.064 4872 Dihedral : 5.596 31.757 3716 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 2.62 % Allowed : 16.91 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.14), residues: 3407 helix: -0.78 (0.19), residues: 649 sheet: -1.56 (0.20), residues: 665 loop : -1.49 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1039 TYR 0.030 0.003 TYR C1067 PHE 0.049 0.003 PHE C 718 TRP 0.014 0.002 TRP B1102 HIS 0.007 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.32 (28009) covalent geometry : angle 0.80978 / 0.42 (38084) SS BOND : bond 0.00386 / 0.28 ( 42) SS BOND : angle 1.96186 / 1.33 ( 84) hydrogen bonds : bond 0.06824 / 4.66 ( 855) hydrogen bonds : angle 7.21098 / 4.89 ( 2358) link_BETA1-4 : bond 0.00353 / 0.17 ( 4) link_BETA1-4 : angle 1.41280 / 0.84 ( 12) link_NAG-ASN : bond 0.00701 / 0.40 ( 28) link_NAG-ASN : angle 3.99090 / 2.81 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8179.69 seconds wall clock time: 140 minutes 48.67 seconds (8448.67 seconds total)