Starting phenix.real_space_refine on Sat Jul 4 17:52:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.map" model { file = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ke9_22835/07_2026/7ke9_22835.cif" } resolution = 3.08 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= 0.058 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 96 5.16 5 C 14244 2.51 5 N 3683 2.21 5 O 4342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.02s 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: 22365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 4.04, per 1000 atoms: 0.18 Number of scatterers: 22365 At special positions: 0 Unit cell: (136.482, 128.018, 179.86, 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 96 16.00 O 4342 8.00 N 3683 7.00 C 14244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.00 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.04 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=2.00 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 819.6 milliseconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 41 sheets defined 28.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.989A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.161A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.786A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.850A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.301A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.512A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.669A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) 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: 3.715A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.293A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.103A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.619A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.580A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.568A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.596A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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: 3.634A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.339A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.936A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.518A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.493A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.675A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.610A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 5.981A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.655A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.313A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.899A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.730A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.545A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.347A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.927A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.801A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.987A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.537A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.170A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.481A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.238A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N PHE B 220 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.748A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.075A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.279A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.592A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.552A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.552A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.201A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.525A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.519A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.347A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.869A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.858A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.640A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.669A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.318A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.452A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5191 1.33 - 1.45: 4688 1.45 - 1.57: 12814 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22813 Sorted by residual: bond pdb=" C5 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 22808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 25045 2.25 - 4.50: 5707 4.50 - 6.75: 323 6.75 - 9.00: 15 9.00 - 11.26: 2 Bond angle restraints: 31092 Sorted by residual: angle pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " pdb=" ND2 ASN B 122 " ideal model delta sigma weight residual 116.40 124.73 -8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " ideal model delta sigma weight residual 112.60 118.05 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " pdb=" CD2 HIS A1064 " ideal model delta sigma weight residual 131.20 124.40 6.80 1.30e+00 5.92e-01 2.74e+01 angle pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " pdb=" CG PHE C 329 " ideal model delta sigma weight residual 113.80 119.03 -5.23 1.00e+00 1.00e+00 2.74e+01 angle pdb=" OE1 GLN A 804 " pdb=" CD GLN A 804 " pdb=" NE2 GLN A 804 " ideal model delta sigma weight residual 122.60 117.39 5.21 1.00e+00 1.00e+00 2.72e+01 ... (remaining 31087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12276 17.85 - 35.69: 625 35.69 - 53.54: 91 53.54 - 71.39: 43 71.39 - 89.23: 20 Dihedral angle restraints: 13055 sinusoidal: 4714 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -171.78 85.78 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.75 85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -167.16 81.16 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 13052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2101 0.073 - 0.146: 1330 0.146 - 0.218: 303 0.218 - 0.291: 81 0.291 - 0.364: 7 Chirality restraints: 3822 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.33e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.23e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.90e+01 ... (remaining 3819 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.234 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" CG ASN A 331 " -0.165 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.498 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.367 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.141 2.00e-02 2.50e+03 1.50e-01 2.81e+02 pdb=" CG ASN C1074 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.129 2.00e-02 2.50e+03 1.36e-01 2.33e+02 pdb=" CG ASN A1074 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.209 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.163 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 10473 2.97 - 3.45: 21326 3.45 - 3.94: 36843 3.94 - 4.42: 40739 4.42 - 4.90: 69919 Nonbonded interactions: 179300 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.491 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.496 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.518 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.518 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.523 3.040 ... (remaining 179295 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and ( \ name N or name CA or name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.420 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.040 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.013 0.077 22907 Z= 0.765 Angle : 1.771 11.256 31339 Z= 1.164 Chirality : 0.093 0.364 3822 Planarity : 0.013 0.158 3929 Dihedral : 12.227 89.234 7552 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.79 % Favored : 93.99 % Rotamer: Outliers : 0.04 % Allowed : 0.71 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2797 helix: -0.43 (0.17), residues: 670 sheet: 0.38 (0.24), residues: 435 loop : -0.81 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.115 0.019 TYR C 917 PHE 0.104 0.012 PHE A 718 TRP 0.108 0.024 TRP C 886 HIS 0.015 0.004 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01342 / 0.77 (22813) covalent geometry : angle 1.74067 / 1.16 (31092) SS BOND : bond 0.01240 / 0.80 ( 35) SS BOND : angle 2.34429 / 1.70 ( 70) hydrogen bonds : bond 0.14116 / 9.06 ( 995) hydrogen bonds : angle 8.47881 / 5.85 ( 2772) link_BETA1-4 : bond 0.02570 / 1.59 ( 12) link_BETA1-4 : angle 4.39625 / 2.76 ( 36) link_NAG-ASN : bond 0.01262 / 0.80 ( 47) link_NAG-ASN : angle 4.60055 / 3.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.1711 time to fit residues: 82.8092 Evaluate side-chains 126 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 317 ASN A1088 HIS B 957 GLN B1010 GLN C 394 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.134954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094367 restraints weight = 37208.707| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.07 r_work: 0.3247 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22907 Z= 0.140 Angle : 0.696 17.121 31339 Z= 0.349 Chirality : 0.046 0.249 3822 Planarity : 0.004 0.051 3929 Dihedral : 5.737 37.603 3027 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 1.11 % Allowed : 4.87 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 2797 helix: 1.39 (0.20), residues: 656 sheet: 0.07 (0.20), residues: 619 loop : -0.63 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.021 0.002 TYR A 170 PHE 0.021 0.001 PHE B 238 TRP 0.020 0.002 TRP B 64 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (22813) covalent geometry : angle 0.63982 / 0.34 (31092) SS BOND : bond 0.00650 / 0.38 ( 35) SS BOND : angle 1.36602 / 0.79 ( 70) hydrogen bonds : bond 0.04467 / 2.85 ( 995) hydrogen bonds : angle 6.44924 / 4.45 ( 2772) link_BETA1-4 : bond 0.00378 / 0.23 ( 12) link_BETA1-4 : angle 1.61307 / 0.99 ( 36) link_NAG-ASN : bond 0.00466 / 0.29 ( 47) link_NAG-ASN : angle 3.98135 / 2.58 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8047 (mmmt) REVERT: A 324 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: A 394 ASN cc_start: 0.8752 (m-40) cc_final: 0.8192 (t0) REVERT: A 396 TYR cc_start: 0.8385 (m-80) cc_final: 0.7888 (m-80) REVERT: A 408 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.8400 (ptm-80) REVERT: A 452 LEU cc_start: 0.8140 (mp) cc_final: 0.7530 (mm) REVERT: A 453 TYR cc_start: 0.8010 (p90) cc_final: 0.7237 (p90) REVERT: A 979 ASP cc_start: 0.8687 (m-30) cc_final: 0.8403 (t0) REVERT: B 41 LYS cc_start: 0.8067 (mttt) cc_final: 0.7253 (mttt) REVERT: B 202 LYS cc_start: 0.7435 (mptt) cc_final: 0.6972 (mptt) REVERT: B 273 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6547 (mtm-85) REVERT: B 988 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7964 (mp0) REVERT: B 1101 HIS cc_start: 0.8073 (m90) cc_final: 0.7575 (m-70) REVERT: C 100 ILE cc_start: 0.8429 (mt) cc_final: 0.8136 (mm) REVERT: C 105 ILE cc_start: 0.7795 (mt) cc_final: 0.7553 (tt) REVERT: C 238 PHE cc_start: 0.6349 (p90) cc_final: 0.6118 (p90) REVERT: C 334 ASN cc_start: 0.7830 (t0) cc_final: 0.7576 (t0) REVERT: C 571 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (t0) REVERT: C 979 ASP cc_start: 0.8278 (m-30) cc_final: 0.7949 (m-30) REVERT: C 1050 MET cc_start: 0.8748 (ptm) cc_final: 0.8250 (ptm) outliers start: 25 outliers final: 12 residues processed: 175 average time/residue: 0.1506 time to fit residues: 43.3324 Evaluate side-chains 136 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1048 HIS B 957 GLN B1048 HIS C 965 GLN C1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091936 restraints weight = 36878.292| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.92 r_work: 0.3272 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22907 Z= 0.149 Angle : 0.605 13.560 31339 Z= 0.302 Chirality : 0.044 0.227 3822 Planarity : 0.003 0.040 3929 Dihedral : 5.042 35.415 3027 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 1.42 % Allowed : 6.20 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 2797 helix: 1.62 (0.20), residues: 671 sheet: -0.04 (0.19), residues: 631 loop : -0.54 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.021 0.001 TYR C1067 PHE 0.017 0.002 PHE B 238 TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22813) covalent geometry : angle 0.56886 / 0.29 (31092) SS BOND : bond 0.00366 / 0.26 ( 35) SS BOND : angle 1.19836 / 0.72 ( 70) hydrogen bonds : bond 0.03950 / 2.53 ( 995) hydrogen bonds : angle 5.97665 / 4.12 ( 2772) link_BETA1-4 : bond 0.00367 / 0.23 ( 12) link_BETA1-4 : angle 1.19822 / 0.72 ( 36) link_NAG-ASN : bond 0.00331 / 0.19 ( 47) link_NAG-ASN : angle 2.97356 / 1.90 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8184 (mmmt) REVERT: A 324 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5202 (mp0) REVERT: A 374 PHE cc_start: 0.8934 (m-10) cc_final: 0.8609 (m-80) REVERT: A 436 TRP cc_start: 0.8610 (p90) cc_final: 0.8117 (p90) REVERT: A 452 LEU cc_start: 0.8126 (mp) cc_final: 0.7592 (mm) REVERT: A 453 TYR cc_start: 0.7894 (p90) cc_final: 0.7275 (p90) REVERT: A 900 MET cc_start: 0.8612 (mtp) cc_final: 0.8367 (mtp) REVERT: B 41 LYS cc_start: 0.8061 (mttt) cc_final: 0.7218 (mttt) REVERT: B 190 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7665 (mtt90) REVERT: B 202 LYS cc_start: 0.7495 (mptt) cc_final: 0.6916 (mptt) REVERT: B 979 ASP cc_start: 0.8101 (m-30) cc_final: 0.7883 (t0) REVERT: B 988 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7925 (mp0) REVERT: B 1101 HIS cc_start: 0.8121 (m90) cc_final: 0.7638 (m-70) REVERT: C 100 ILE cc_start: 0.8460 (mt) cc_final: 0.8165 (mm) REVERT: C 334 ASN cc_start: 0.8162 (t0) cc_final: 0.7882 (t0) REVERT: C 571 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7831 (t0) REVERT: C 979 ASP cc_start: 0.8302 (m-30) cc_final: 0.8002 (m-30) outliers start: 32 outliers final: 21 residues processed: 162 average time/residue: 0.1510 time to fit residues: 40.3678 Evaluate side-chains 142 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 3 optimal weight: 0.0970 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 131 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095403 restraints weight = 37137.969| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.02 r_work: 0.3299 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 22907 Z= 0.101 Angle : 0.558 12.425 31339 Z= 0.277 Chirality : 0.043 0.232 3822 Planarity : 0.003 0.041 3929 Dihedral : 4.672 32.868 3027 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 1.20 % Allowed : 7.58 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 2797 helix: 1.97 (0.21), residues: 660 sheet: -0.05 (0.20), residues: 573 loop : -0.42 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE B 168 TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (22813) covalent geometry : angle 0.52355 / 0.27 (31092) SS BOND : bond 0.00197 / 0.12 ( 35) SS BOND : angle 1.81716 / 1.04 ( 70) hydrogen bonds : bond 0.03566 / 2.30 ( 995) hydrogen bonds : angle 5.65170 / 3.90 ( 2772) link_BETA1-4 : bond 0.00378 / 0.24 ( 12) link_BETA1-4 : angle 1.07671 / 0.65 ( 36) link_NAG-ASN : bond 0.00344 / 0.20 ( 47) link_NAG-ASN : angle 2.59871 / 1.64 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8275 (mmmt) REVERT: A 374 PHE cc_start: 0.8840 (m-10) cc_final: 0.8552 (m-80) REVERT: A 436 TRP cc_start: 0.8666 (p90) cc_final: 0.8235 (p90) REVERT: A 452 LEU cc_start: 0.8017 (mp) cc_final: 0.7513 (mm) REVERT: A 453 TYR cc_start: 0.7867 (p90) cc_final: 0.7060 (p90) REVERT: A 900 MET cc_start: 0.8548 (mtp) cc_final: 0.8318 (mtp) REVERT: B 129 LYS cc_start: 0.6553 (tptt) cc_final: 0.6251 (tptp) REVERT: B 190 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7699 (mtt90) REVERT: B 202 LYS cc_start: 0.7502 (mptt) cc_final: 0.6900 (mptt) REVERT: B 273 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5709 (mtt-85) REVERT: B 988 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7850 (mp0) REVERT: B 1050 MET cc_start: 0.8715 (ptm) cc_final: 0.8409 (ptm) REVERT: B 1101 HIS cc_start: 0.8106 (m90) cc_final: 0.7613 (m-70) REVERT: C 100 ILE cc_start: 0.8499 (mt) cc_final: 0.8220 (mm) REVERT: C 238 PHE cc_start: 0.6569 (p90) cc_final: 0.6148 (p90) REVERT: C 334 ASN cc_start: 0.8188 (t0) cc_final: 0.7896 (t0) REVERT: C 369 TYR cc_start: 0.8399 (t80) cc_final: 0.8080 (t80) REVERT: C 571 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7751 (t0) REVERT: C 697 MET cc_start: 0.8859 (ptm) cc_final: 0.8612 (ptm) REVERT: C 979 ASP cc_start: 0.8299 (m-30) cc_final: 0.8020 (m-30) outliers start: 27 outliers final: 19 residues processed: 166 average time/residue: 0.1514 time to fit residues: 41.6005 Evaluate side-chains 143 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 40 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 227 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092448 restraints weight = 36639.271| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.91 r_work: 0.3280 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22907 Z= 0.139 Angle : 0.541 11.583 31339 Z= 0.270 Chirality : 0.043 0.242 3822 Planarity : 0.003 0.041 3929 Dihedral : 4.485 32.856 3027 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.46 % Allowed : 8.29 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2797 helix: 1.94 (0.20), residues: 663 sheet: -0.14 (0.20), residues: 601 loop : -0.39 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.018 0.001 TYR A1067 PHE 0.025 0.001 PHE B 168 TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22813) covalent geometry : angle 0.51297 / 0.26 (31092) SS BOND : bond 0.00238 / 0.15 ( 35) SS BOND : angle 1.35104 / 0.81 ( 70) hydrogen bonds : bond 0.03562 / 2.29 ( 995) hydrogen bonds : angle 5.53306 / 3.83 ( 2772) link_BETA1-4 : bond 0.00334 / 0.20 ( 12) link_BETA1-4 : angle 1.00371 / 0.61 ( 36) link_NAG-ASN : bond 0.00319 / 0.19 ( 47) link_NAG-ASN : angle 2.43445 / 1.53 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8287 (mmmt) REVERT: A 357 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8298 (tpp80) REVERT: A 374 PHE cc_start: 0.8847 (m-10) cc_final: 0.8593 (m-80) REVERT: A 436 TRP cc_start: 0.8708 (p90) cc_final: 0.8315 (p90) REVERT: A 452 LEU cc_start: 0.7735 (mp) cc_final: 0.6774 (mm) REVERT: A 453 TYR cc_start: 0.7724 (p90) cc_final: 0.7016 (p90) REVERT: A 492 LEU cc_start: 0.8948 (mt) cc_final: 0.8550 (tp) REVERT: B 64 TRP cc_start: 0.7723 (t60) cc_final: 0.7517 (t60) REVERT: B 129 LYS cc_start: 0.6532 (tptt) cc_final: 0.6258 (tppt) REVERT: B 190 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7720 (mtt90) REVERT: B 202 LYS cc_start: 0.7568 (mptt) cc_final: 0.6943 (mptt) REVERT: B 273 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5919 (mtt-85) REVERT: B 979 ASP cc_start: 0.8184 (t0) cc_final: 0.7801 (t0) REVERT: B 988 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7865 (mp0) REVERT: B 1101 HIS cc_start: 0.8140 (m90) cc_final: 0.7658 (m-70) REVERT: C 100 ILE cc_start: 0.8490 (mt) cc_final: 0.8224 (mm) REVERT: C 334 ASN cc_start: 0.8240 (t0) cc_final: 0.7940 (t0) REVERT: C 369 TYR cc_start: 0.8327 (t80) cc_final: 0.8041 (t80) REVERT: C 571 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7755 (t0) REVERT: C 697 MET cc_start: 0.8834 (ptm) cc_final: 0.8604 (ptm) REVERT: C 979 ASP cc_start: 0.8311 (m-30) cc_final: 0.8049 (m-30) outliers start: 33 outliers final: 25 residues processed: 161 average time/residue: 0.1493 time to fit residues: 39.8437 Evaluate side-chains 146 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 89 optimal weight: 0.9980 chunk 128 optimal weight: 30.0000 chunk 270 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 158 optimal weight: 0.0020 chunk 134 optimal weight: 0.0170 chunk 252 optimal weight: 0.9980 chunk 268 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 chunk 204 optimal weight: 3.9990 overall best weight: 0.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.138398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097411 restraints weight = 37235.063| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.95 r_work: 0.3326 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22907 Z= 0.094 Angle : 0.511 10.917 31339 Z= 0.256 Chirality : 0.042 0.235 3822 Planarity : 0.003 0.042 3929 Dihedral : 4.291 32.127 3027 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.42 % Allowed : 8.60 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2797 helix: 2.10 (0.20), residues: 665 sheet: -0.08 (0.20), residues: 583 loop : -0.29 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE B 168 TRP 0.008 0.001 TRP A 64 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (22813) covalent geometry : angle 0.48658 / 0.25 (31092) SS BOND : bond 0.00365 / 0.28 ( 35) SS BOND : angle 1.19936 / 0.73 ( 70) hydrogen bonds : bond 0.03344 / 2.16 ( 995) hydrogen bonds : angle 5.35051 / 3.70 ( 2772) link_BETA1-4 : bond 0.00368 / 0.22 ( 12) link_BETA1-4 : angle 0.93493 / 0.57 ( 36) link_NAG-ASN : bond 0.00328 / 0.20 ( 47) link_NAG-ASN : angle 2.22503 / 1.38 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8275 (mmmt) REVERT: A 357 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8279 (tpp80) REVERT: A 374 PHE cc_start: 0.8823 (m-10) cc_final: 0.8584 (m-80) REVERT: A 436 TRP cc_start: 0.8698 (p90) cc_final: 0.8318 (p90) REVERT: A 452 LEU cc_start: 0.7590 (mp) cc_final: 0.6699 (mm) REVERT: A 453 TYR cc_start: 0.7651 (p90) cc_final: 0.6955 (p90) REVERT: A 468 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 492 LEU cc_start: 0.8965 (mt) cc_final: 0.8564 (tp) REVERT: B 129 LYS cc_start: 0.6651 (tptt) cc_final: 0.6360 (tppt) REVERT: B 190 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7845 (mtt90) REVERT: B 202 LYS cc_start: 0.7540 (mptt) cc_final: 0.6950 (mptt) REVERT: B 269 TYR cc_start: 0.8003 (m-10) cc_final: 0.7503 (m-80) REVERT: B 273 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.5892 (mtm-85) REVERT: B 568 ASP cc_start: 0.8465 (m-30) cc_final: 0.8214 (m-30) REVERT: B 979 ASP cc_start: 0.8272 (t0) cc_final: 0.7866 (t0) REVERT: B 988 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7678 (mp0) REVERT: B 1050 MET cc_start: 0.8723 (ptm) cc_final: 0.8395 (ptm) REVERT: B 1101 HIS cc_start: 0.8130 (m90) cc_final: 0.7652 (m-70) REVERT: C 100 ILE cc_start: 0.8440 (mt) cc_final: 0.8154 (mm) REVERT: C 105 ILE cc_start: 0.7887 (mt) cc_final: 0.7551 (tt) REVERT: C 334 ASN cc_start: 0.8245 (t0) cc_final: 0.7912 (t0) REVERT: C 571 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7737 (t0) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 0.1458 time to fit residues: 40.0856 Evaluate side-chains 154 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090708 restraints weight = 37061.433| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.91 r_work: 0.3249 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22907 Z= 0.256 Angle : 0.604 10.822 31339 Z= 0.302 Chirality : 0.045 0.249 3822 Planarity : 0.004 0.086 3929 Dihedral : 4.494 33.625 3027 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.55 % Allowed : 9.13 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2797 helix: 1.73 (0.20), residues: 666 sheet: -0.21 (0.19), residues: 638 loop : -0.42 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.022 0.002 TYR A1067 PHE 0.022 0.002 PHE C 201 TRP 0.007 0.001 TRP C 886 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (22813) covalent geometry : angle 0.57981 / 0.30 (31092) SS BOND : bond 0.00353 / 0.24 ( 35) SS BOND : angle 1.40059 / 0.87 ( 70) hydrogen bonds : bond 0.03823 / 2.45 ( 995) hydrogen bonds : angle 5.67309 / 3.91 ( 2772) link_BETA1-4 : bond 0.00229 / 0.11 ( 12) link_BETA1-4 : angle 0.92761 / 0.56 ( 36) link_NAG-ASN : bond 0.00359 / 0.20 ( 47) link_NAG-ASN : angle 2.37269 / 1.50 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8240 (mmmt) REVERT: A 357 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8366 (mmm-85) REVERT: A 374 PHE cc_start: 0.8891 (m-10) cc_final: 0.8662 (m-80) REVERT: A 436 TRP cc_start: 0.8720 (p90) cc_final: 0.8518 (p90) REVERT: A 452 LEU cc_start: 0.7650 (mp) cc_final: 0.6078 (mt) REVERT: A 453 TYR cc_start: 0.7829 (p90) cc_final: 0.7227 (p90) REVERT: A 468 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 492 LEU cc_start: 0.8899 (mt) cc_final: 0.8404 (tp) REVERT: B 190 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7863 (mtt90) REVERT: B 202 LYS cc_start: 0.7560 (mptt) cc_final: 0.6966 (mptt) REVERT: B 273 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6275 (mtm-85) REVERT: B 979 ASP cc_start: 0.8376 (t0) cc_final: 0.8034 (t0) REVERT: B 988 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7991 (mp0) REVERT: B 1101 HIS cc_start: 0.8170 (m90) cc_final: 0.7705 (m-70) REVERT: C 100 ILE cc_start: 0.8414 (mt) cc_final: 0.8131 (mm) REVERT: C 334 ASN cc_start: 0.8273 (t0) cc_final: 0.8070 (t0) REVERT: C 369 TYR cc_start: 0.8024 (t80) cc_final: 0.7816 (t80) REVERT: C 571 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7893 (t0) outliers start: 35 outliers final: 24 residues processed: 144 average time/residue: 0.1530 time to fit residues: 36.4757 Evaluate side-chains 142 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 223 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN C 901 GLN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.133072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093353 restraints weight = 36673.633| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.05 r_work: 0.3293 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22907 Z= 0.115 Angle : 0.533 13.245 31339 Z= 0.267 Chirality : 0.043 0.289 3822 Planarity : 0.003 0.074 3929 Dihedral : 4.321 32.352 3027 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.20 % Allowed : 9.48 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2797 helix: 1.92 (0.20), residues: 671 sheet: -0.11 (0.20), residues: 615 loop : -0.39 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.018 0.001 TYR B1067 PHE 0.022 0.001 PHE A 592 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (22813) covalent geometry : angle 0.50386 / 0.26 (31092) SS BOND : bond 0.00195 / 0.12 ( 35) SS BOND : angle 2.17539 / 1.26 ( 70) hydrogen bonds : bond 0.03432 / 2.20 ( 995) hydrogen bonds : angle 5.45637 / 3.76 ( 2772) link_BETA1-4 : bond 0.00336 / 0.20 ( 12) link_BETA1-4 : angle 0.87820 / 0.53 ( 36) link_NAG-ASN : bond 0.00320 / 0.19 ( 47) link_NAG-ASN : angle 2.17146 / 1.35 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8245 (mmmt) REVERT: A 374 PHE cc_start: 0.8851 (m-10) cc_final: 0.8610 (m-80) REVERT: A 436 TRP cc_start: 0.8676 (p90) cc_final: 0.8312 (p90) REVERT: A 452 LEU cc_start: 0.7547 (mp) cc_final: 0.5994 (mt) REVERT: A 453 TYR cc_start: 0.7775 (p90) cc_final: 0.7198 (p90) REVERT: A 468 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 492 LEU cc_start: 0.8936 (mt) cc_final: 0.8405 (tp) REVERT: B 190 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7879 (mtt90) REVERT: B 202 LYS cc_start: 0.7518 (mptt) cc_final: 0.6935 (mptt) REVERT: B 273 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6244 (mtm-85) REVERT: B 568 ASP cc_start: 0.8523 (m-30) cc_final: 0.8153 (m-30) REVERT: B 735 SER cc_start: 0.9032 (t) cc_final: 0.8501 (p) REVERT: B 979 ASP cc_start: 0.8209 (t0) cc_final: 0.7916 (t0) REVERT: B 988 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7685 (mp0) REVERT: B 994 ASP cc_start: 0.8192 (p0) cc_final: 0.7730 (m-30) REVERT: B 1050 MET cc_start: 0.8761 (ptm) cc_final: 0.8433 (ptm) REVERT: B 1101 HIS cc_start: 0.8121 (m90) cc_final: 0.7630 (m-70) REVERT: C 100 ILE cc_start: 0.8407 (mt) cc_final: 0.8116 (mm) REVERT: C 334 ASN cc_start: 0.8248 (t0) cc_final: 0.8036 (t0) REVERT: C 369 TYR cc_start: 0.8189 (t80) cc_final: 0.7979 (t80) REVERT: C 571 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7770 (t0) outliers start: 27 outliers final: 23 residues processed: 152 average time/residue: 0.1488 time to fit residues: 37.4215 Evaluate side-chains 147 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3129 > 50: distance: 4 - 7: 4.266 distance: 7 - 8: 4.576 distance: 7 - 60: 13.165 distance: 8 - 9: 3.600 distance: 8 - 11: 4.168 distance: 9 - 10: 18.311 distance: 9 - 15: 8.756 distance: 10 - 57: 13.810 distance: 11 - 12: 5.194 distance: 11 - 13: 11.488 distance: 12 - 14: 13.669 distance: 15 - 175: 9.942 distance: 16 - 17: 10.052 distance: 17 - 18: 3.929 distance: 17 - 21: 10.439 distance: 19 - 20: 5.613 distance: 20 - 164: 7.969 distance: 21 - 22: 11.740 distance: 22 - 23: 20.376 distance: 22 - 25: 6.596 distance: 23 - 24: 12.483 distance: 23 - 31: 10.724 distance: 25 - 26: 8.378 distance: 26 - 27: 11.422 distance: 26 - 28: 3.964 distance: 27 - 29: 10.510 distance: 28 - 30: 11.694 distance: 29 - 30: 7.658 distance: 31 - 32: 10.385 distance: 32 - 33: 8.079 distance: 32 - 35: 4.288 distance: 33 - 34: 9.375 distance: 33 - 39: 9.621 distance: 35 - 36: 8.490 distance: 36 - 37: 10.204 distance: 36 - 38: 9.557 distance: 39 - 40: 6.947 distance: 40 - 41: 7.536 distance: 41 - 42: 6.646 distance: 41 - 43: 13.947 distance: 43 - 44: 8.049 distance: 44 - 45: 10.797 distance: 44 - 47: 7.702 distance: 45 - 46: 29.157 distance: 45 - 52: 32.590 distance: 47 - 48: 8.132 distance: 48 - 49: 10.663 distance: 49 - 50: 10.511 distance: 50 - 51: 23.065 distance: 52 - 53: 17.156 distance: 52 - 153: 28.860 distance: 53 - 54: 18.760 distance: 53 - 56: 41.780 distance: 54 - 55: 9.720 distance: 54 - 57: 7.718 distance: 57 - 58: 7.997 distance: 58 - 59: 10.930 distance: 58 - 61: 7.928 distance: 59 - 60: 11.813 distance: 59 - 67: 12.745 distance: 61 - 62: 9.968 distance: 62 - 63: 9.762 distance: 62 - 64: 11.360 distance: 63 - 65: 10.742 distance: 64 - 66: 15.280 distance: 65 - 66: 5.455 distance: 67 - 68: 13.446 distance: 68 - 69: 9.967 distance: 68 - 71: 10.494 distance: 69 - 70: 3.688 distance: 69 - 78: 6.590 distance: 71 - 72: 3.941 distance: 72 - 73: 14.484 distance: 72 - 74: 16.150 distance: 73 - 75: 13.992 distance: 74 - 76: 22.156 distance: 75 - 77: 14.271 distance: 76 - 77: 19.578 distance: 78 - 79: 5.262 distance: 78 - 84: 7.524 distance: 79 - 80: 9.161 distance: 79 - 82: 12.285 distance: 80 - 81: 18.052 distance: 80 - 85: 11.228 distance: 82 - 83: 12.508 distance: 83 - 84: 10.978