Starting phenix.real_space_refine on Fri Mar 6 00:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8m_24318/03_2026/7r8m_24318.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 116 5.16 5 C 16774 2.51 5 N 4321 2.21 5 O 5112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26323 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7386 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 9, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7643 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 54, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'TYR:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 137 Chain: "C" Number of atoms: 7352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7352 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 52, 'TRANS': 925} Chain breaks: 11 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 213 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 804 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 804 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.30, per 1000 atoms: 0.24 Number of scatterers: 26323 At special positions: 0 Unit cell: (135.564, 132.088, 188.573, 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 116 16.00 O 5112 8.00 N 4321 7.00 C 16774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 165 " " NAG F 1 " - " ASN B 282 " " NAG G 1 " - " ASN B 343 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN C 282 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 55 sheets defined 22.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.662A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.907A pdb=" N ILE A 418 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.650A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.949A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.715A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.566A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.576A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 985 through 1029 Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.291A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.554A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.631A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.586A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.325A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.115A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.792A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.746A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.729A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 945 removed outlier: 3.642A pdb=" N LEU B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.664A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.335A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.306A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.551A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.087A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.661A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.673A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY C 889 " --> 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 removed outlier: 3.729A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.707A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.876A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.110A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.623A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.630A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.844A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.770A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.832A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.802A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.802A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.470A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.706A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.786A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.967A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.761A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.831A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.324A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.514A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.884A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 7.847A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.640A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.887A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.887A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.581A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.629A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.537A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.575A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 665 through 667 removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 727 removed outlier: 7.231A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.536A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 224 through 229 removed outlier: 7.035A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.927A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 326 through 327 removed outlier: 3.539A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 665 through 667 Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.589A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.691A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.622A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 7.040A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 90 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.712A pdb=" N LEU D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.366A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AF3, first strand: chain 'E' and resid 35 through 38 removed outlier: 6.708A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 89 through 90 removed outlier: 3.596A pdb=" N VAL E 97 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.559A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE H 50 " --> pdb=" O ARG H 58 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.559A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 96 " --> pdb=" O PHE H 100B" (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE H 100B" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 20 through 23 Processing sheet with id=AF8, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.578A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 44 through 49 removed outlier: 6.831A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2259 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: 5.46 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8390 1.34 - 1.47: 6713 1.47 - 1.60: 11657 1.60 - 1.72: 1 1.72 - 1.85: 146 Bond restraints: 26907 Sorted by residual: bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.18e-02 7.18e+03 1.21e+01 bond pdb=" N VAL A 615 " pdb=" CA VAL A 615 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 ... (remaining 26902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 36058 2.65 - 5.31: 588 5.31 - 7.96: 40 7.96 - 10.61: 4 10.61 - 13.27: 2 Bond angle restraints: 36692 Sorted by residual: angle pdb=" N GLU B 340 " pdb=" CA GLU B 340 " pdb=" C GLU B 340 " ideal model delta sigma weight residual 113.20 103.54 9.66 1.21e+00 6.83e-01 6.38e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 121.48 134.75 -13.27 2.04e+00 2.40e-01 4.23e+01 angle pdb=" N ILE C 128 " pdb=" CA ILE C 128 " pdb=" C ILE C 128 " ideal model delta sigma weight residual 111.88 105.00 6.88 1.06e+00 8.90e-01 4.22e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 113.20 108.53 4.67 9.60e-01 1.09e+00 2.36e+01 angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 111.14 105.89 5.25 1.08e+00 8.57e-01 2.36e+01 ... (remaining 36687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14776 17.87 - 35.73: 1295 35.73 - 53.60: 229 53.60 - 71.47: 47 71.47 - 89.33: 35 Dihedral angle restraints: 16382 sinusoidal: 6496 harmonic: 9886 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.67 -89.33 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -172.29 86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 178.91 -85.91 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 16379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4283 0.164 - 0.327: 41 0.327 - 0.491: 3 0.491 - 0.655: 1 0.655 - 0.818: 1 Chirality restraints: 4329 Sorted by residual: 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 -2.31 -0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.67e+00 ... (remaining 4326 not shown) Planarity restraints: 4721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.362 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG C1304 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.139 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.551 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.335 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG K 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.317 2.00e-02 2.50e+03 2.77e-01 9.56e+02 pdb=" C7 NAG J 2 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.119 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.128 2.00e-02 2.50e+03 ... (remaining 4718 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 212 2.53 - 3.12: 20834 3.12 - 3.71: 41267 3.71 - 4.31: 57306 4.31 - 4.90: 94141 Nonbonded interactions: 213760 Sorted by model distance: nonbonded pdb=" O3 NAG B1301 " pdb=" O7 NAG B1301 " model vdw 1.934 3.040 nonbonded pdb=" O3 NAG C1306 " pdb=" O7 NAG C1306 " model vdw 2.016 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.041 3.040 nonbonded pdb=" O TRP D 47 " pdb=" OG SER D 60 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A1117 " pdb=" OD1 ASP A1139 " model vdw 2.137 3.040 ... (remaining 213755 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 through 130 and (name N or name CA or name C or name O or name CB )) o \ r resid 131 through 140 or (resid 157 through 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 187 or (resid 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or resid 191 through 194 or (resi \ d 195 through 198 and (name N or name CA or name C or name O or name CB )) or re \ sid 199 through 217 or (resid 218 and (name N or name CA or name C or name O or \ name CB )) or resid 219 through 236 or (resid 237 and (name N or name CA or name \ C or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or \ name C or name O or name CB )) or resid 240 through 243 or resid 264 through 280 \ or (resid 281 and (name N or name CA or name C or name O or name CB )) or resid \ 282 through 331 or (resid 332 through 335 and (name N or name CA or name C or n \ ame O or name CB )) or resid 336 through 350 or (resid 351 through 352 and (name \ N or name CA or name C or name O or name CB )) or resid 353 through 363 or (res \ id 364 and (name N or name CA or name C or name O or name CB )) or resid 365 thr \ ough 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) \ or resid 370 through 373 or (resid 374 and (name N or name CA or name C or name \ O or name CB )) or resid 375 through 407 or (resid 408 and (name N or name CA or \ name C or name O or name CB )) or resid 409 through 439 or (resid 440 through 4 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 450 through \ 496 or (resid 497 through 498 and (name N or name CA or name C or name O or nam \ e CB )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 508 or (resid 509 and (name N or na \ me CA or name C or name O or name CB )) or resid 510 through 620 or resid 641 th \ rough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 736 or (resid 737 and (name N or name CA or name C or name \ O or name CB )) or resid 738 through 740 or (resid 741 and (name N or name CA o \ r name C or name O or name CB )) or resid 742 through 813 or (resid 814 and (nam \ e N or name CA or name C or name O or name CB )) or resid 815 through 827 or res \ id 856 through 1304)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 throug \ h 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thro \ ugh 140 or (resid 157 through 160 and (name N or name CA or name C or name O or \ name CB )) or resid 161 through 175 or (resid 176 through 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 195 or (resid 196 th \ rough 198 and (name N or name CA or name C or name O or name CB )) or resid 199 \ through 236 or (resid 237 and (name N or name CA or name C or name O or name CB \ )) or resid 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 289 or (resid 290 and (name N or name CA or name C o \ r name O or name CB )) or resid 291 through 297 or (resid 298 and (name N or nam \ e CA or name C or name O or name CB )) or resid 299 through 332 or (resid 333 th \ rough 335 and (name N or name CA or name C or name O or name CB )) or resid 336 \ through 339 or (resid 340 and (name N or name CA or name C or name O or name CB \ )) or resid 341 through 345 or (resid 346 and (name N or name CA or name C or na \ me O or name CB )) or resid 347 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 or (resid 351 through 352 and (n \ ame N or name CA or name C or name O or name CB )) or resid 353 through 363 or ( \ resid 364 and (name N or name CA or name C or name O or name CB )) or resid 365 \ through 373 or (resid 374 and (name N or name CA or name C or name O or name CB \ )) or resid 375 through 397 or (resid 398 and (name N or name CA or name C or na \ me O or name CB )) or resid 399 through 404 or (resid 405 through 408 and (name \ N or name CA or name C or name O or name CB )) or resid 409 through 413 or (resi \ d 414 through 415 and (name N or name CA or name C or name O or name CB )) or re \ sid 416 through 426 or (resid 427 through 428 and (name N or name CA or name C o \ r name O or name CB )) or resid 429 through 440 or (resid 441 through 443 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 449 and (name N or \ name CA or name C or name O or name CB )) or resid 450 through 453 or (resid 454 \ and (name N or name CA or name C or name O or name CB )) or resid 491 or (resid \ 492 through 493 and (name N or name CA or name C or name O or name CB )) or res \ id 494 through 496 or (resid 497 through 498 and (name N or name CA or name C or \ name O or name CB )) or resid 503 through 508 or (resid 509 and (name N or name \ CA or name C or name O or name CB )) or resid 510 through 527 or (resid 528 thr \ ough 529 and (name N or name CA or name C or name O or name CB )) or resid 530 t \ hrough 620 or resid 641 through 701 or (resid 702 and (name N or name CA or name \ C or name O or name CB )) or resid 703 through 724 or (resid 725 and (name N or \ name CA or name C or name O or name CB )) or resid 726 through 736 or (resid 73 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 738 through \ 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) or re \ sid 815 through 827 or resid 856 through 993 or (resid 994 and (name N or name C \ A or name C or name O or name CB )) or resid 995 through 1304)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 95 or resid \ 99 through 187 or (resid 188 and (name N or name CA or name C or name O or name \ CB )) or resid 189 through 217 or (resid 218 and (name N or name CA or name C o \ r name O or name CB )) or resid 219 through 243 or resid 264 through 280 or (res \ id 281 and (name N or name CA or name C or name O or name CB )) or resid 282 thr \ ough 297 or (resid 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 through 439 or (resid 440 through 449 and (name N o \ r name CA or name C or name O or name CB )) or resid 450 through 454 or resid 49 \ 1 through 504 or (resid 505 and (name N or name CA or name C or name O or name C \ B )) or resid 506 through 724 or (resid 725 and (name N or name CA or name C or \ name O or name CB )) or resid 726 through 740 or (resid 741 and (name N or name \ CA or name C or name O or name CB )) or resid 742 through 827 or resid 856 throu \ gh 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 5.780 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: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.006 0.655 26978 Z= 0.472 Angle : 0.818 22.190 36865 Z= 0.444 Chirality : 0.055 0.818 4329 Planarity : 0.016 0.310 4694 Dihedral : 13.809 88.669 9907 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 0.54 % Allowed : 0.89 % Favored : 98.57 % 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: -1.74 (0.14), residues: 3339 helix: 0.03 (0.21), residues: 636 sheet: -1.37 (0.21), residues: 608 loop : -1.51 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.023 0.001 TYR A 365 PHE 0.038 0.002 PHE H 100B TRP 0.034 0.002 TRP E 35 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00441 (26907) covalent geometry : angle 0.75441 (36692) SS BOND : bond 0.00334 ( 37) SS BOND : angle 1.70010 ( 74) hydrogen bonds : bond 0.22140 ( 855) hydrogen bonds : angle 9.19132 ( 2259) Misc. bond : bond 0.65458 ( 1) link_BETA1-4 : bond 0.01448 ( 5) link_BETA1-4 : angle 4.50171 ( 15) link_BETA1-6 : bond 0.00085 ( 1) link_BETA1-6 : angle 3.90087 ( 3) link_NAG-ASN : bond 0.01824 ( 27) link_NAG-ASN : angle 6.27856 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 432 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1079 PRO cc_start: 0.6438 (Cg_exo) cc_final: 0.6135 (Cg_endo) REVERT: B 106 PHE cc_start: 0.3483 (m-80) cc_final: 0.3219 (m-80) REVERT: B 201 PHE cc_start: 0.7126 (t80) cc_final: 0.6917 (t80) REVERT: B 220 PHE cc_start: 0.7516 (p90) cc_final: 0.7175 (p90) REVERT: C 574 ASP cc_start: 0.7133 (p0) cc_final: 0.6820 (p0) REVERT: C 882 ILE cc_start: 0.8619 (pt) cc_final: 0.8415 (pt) REVERT: E 32 ASP cc_start: 0.8108 (t70) cc_final: 0.7641 (t70) REVERT: H 103 TRP cc_start: 0.7612 (m-10) cc_final: 0.7283 (m-10) REVERT: L 8 PRO cc_start: 0.6315 (Cg_endo) cc_final: 0.6106 (Cg_exo) REVERT: L 21 ILE cc_start: 0.5997 (mm) cc_final: 0.5586 (mp) REVERT: L 33 VAL cc_start: 0.7511 (t) cc_final: 0.7237 (t) outliers start: 15 outliers final: 5 residues processed: 442 average time/residue: 0.1533 time to fit residues: 114.0599 Evaluate side-chains 299 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 294 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 613 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.162293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129362 restraints weight = 59534.097| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.73 r_work: 0.3703 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26978 Z= 0.168 Angle : 0.699 11.062 36865 Z= 0.348 Chirality : 0.048 0.318 4329 Planarity : 0.005 0.054 4694 Dihedral : 7.133 59.234 4308 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 1.14 % Allowed : 10.94 % Favored : 87.91 % 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: -1.75 (0.14), residues: 3339 helix: -0.02 (0.20), residues: 651 sheet: -1.29 (0.20), residues: 646 loop : -1.53 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 94 TYR 0.026 0.002 TYR B 453 PHE 0.025 0.002 PHE B 429 TRP 0.027 0.002 TRP D 36 HIS 0.015 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00361 (26907) covalent geometry : angle 0.67625 (36692) SS BOND : bond 0.00544 ( 37) SS BOND : angle 1.69342 ( 74) hydrogen bonds : bond 0.05202 ( 855) hydrogen bonds : angle 7.20086 ( 2259) Misc. bond : bond 0.00368 ( 1) link_BETA1-4 : bond 0.01130 ( 5) link_BETA1-4 : angle 3.58005 ( 15) link_BETA1-6 : bond 0.00459 ( 1) link_BETA1-6 : angle 2.93839 ( 3) link_NAG-ASN : bond 0.00563 ( 27) link_NAG-ASN : angle 3.16509 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5395 (mm) cc_final: 0.5152 (mt) REVERT: A 223 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7329 (mm) REVERT: A 275 PHE cc_start: 0.8070 (m-80) cc_final: 0.7812 (m-10) REVERT: A 768 THR cc_start: 0.8880 (m) cc_final: 0.8649 (m) REVERT: A 973 ILE cc_start: 0.7076 (tp) cc_final: 0.6838 (tp) REVERT: A 1031 GLU cc_start: 0.7164 (tt0) cc_final: 0.6882 (pt0) REVERT: A 1079 PRO cc_start: 0.7055 (Cg_exo) cc_final: 0.6711 (Cg_endo) REVERT: B 84 LEU cc_start: 0.5052 (mt) cc_final: 0.4610 (mt) REVERT: B 220 PHE cc_start: 0.7565 (p90) cc_final: 0.7137 (p90) REVERT: B 346 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7995 (tpp80) REVERT: B 495 TYR cc_start: 0.5353 (t80) cc_final: 0.4987 (t80) REVERT: B 985 ASP cc_start: 0.7918 (p0) cc_final: 0.7673 (p0) REVERT: C 104 TRP cc_start: 0.4901 (m-10) cc_final: 0.4457 (m-10) REVERT: C 280 ASN cc_start: 0.8505 (t0) cc_final: 0.8085 (t0) REVERT: C 347 PHE cc_start: 0.7847 (m-80) cc_final: 0.7547 (m-80) REVERT: E 4 LEU cc_start: 0.5225 (mt) cc_final: 0.5013 (mt) REVERT: E 54 ARG cc_start: 0.4812 (mmt-90) cc_final: 0.2577 (mtp180) REVERT: E 73 LEU cc_start: 0.6431 (tp) cc_final: 0.6077 (tp) REVERT: H 50 ILE cc_start: 0.8303 (mm) cc_final: 0.7972 (tp) REVERT: H 103 TRP cc_start: 0.7604 (m100) cc_final: 0.7255 (m-10) REVERT: L 21 ILE cc_start: 0.4815 (mm) cc_final: 0.4553 (mp) REVERT: L 49 TYR cc_start: 0.8501 (p90) cc_final: 0.8174 (p90) outliers start: 32 outliers final: 25 residues processed: 376 average time/residue: 0.1497 time to fit residues: 94.7678 Evaluate side-chains 329 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 198 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 284 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.161961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128878 restraints weight = 59490.898| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.66 r_work: 0.3697 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26978 Z= 0.147 Angle : 0.633 12.460 36865 Z= 0.316 Chirality : 0.046 0.431 4329 Planarity : 0.005 0.054 4694 Dihedral : 6.601 59.116 4307 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.62 % Favored : 93.32 % Rotamer: Outliers : 2.00 % Allowed : 13.52 % Favored : 84.48 % 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: -1.67 (0.14), residues: 3339 helix: 0.12 (0.20), residues: 645 sheet: -1.26 (0.21), residues: 656 loop : -1.50 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.026 0.001 TYR B 453 PHE 0.018 0.001 PHE C 86 TRP 0.013 0.002 TRP D 36 HIS 0.012 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00325 (26907) covalent geometry : angle 0.61182 (36692) SS BOND : bond 0.00408 ( 37) SS BOND : angle 1.62081 ( 74) hydrogen bonds : bond 0.04833 ( 855) hydrogen bonds : angle 6.71352 ( 2259) Misc. bond : bond 0.00094 ( 1) link_BETA1-4 : bond 0.01129 ( 5) link_BETA1-4 : angle 3.27974 ( 15) link_BETA1-6 : bond 0.00412 ( 1) link_BETA1-6 : angle 2.21189 ( 3) link_NAG-ASN : bond 0.00409 ( 27) link_NAG-ASN : angle 2.89108 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5516 (mm) cc_final: 0.5252 (mt) REVERT: A 223 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6922 (mm) REVERT: A 275 PHE cc_start: 0.8234 (m-80) cc_final: 0.7850 (m-10) REVERT: A 973 ILE cc_start: 0.6944 (tp) cc_final: 0.6656 (tp) REVERT: A 1031 GLU cc_start: 0.7093 (tt0) cc_final: 0.6810 (pt0) REVERT: B 194 PHE cc_start: 0.6263 (m-10) cc_final: 0.5890 (m-10) REVERT: B 220 PHE cc_start: 0.7566 (p90) cc_final: 0.7118 (p90) REVERT: B 495 TYR cc_start: 0.5217 (t80) cc_final: 0.4957 (t80) REVERT: B 900 MET cc_start: 0.7667 (mtp) cc_final: 0.7402 (mtp) REVERT: B 1139 ASP cc_start: 0.7860 (m-30) cc_final: 0.7656 (m-30) REVERT: C 104 TRP cc_start: 0.5002 (m-10) cc_final: 0.4560 (m-10) REVERT: C 280 ASN cc_start: 0.8578 (t0) cc_final: 0.8126 (t0) REVERT: C 347 PHE cc_start: 0.7773 (m-80) cc_final: 0.7456 (m-80) REVERT: C 1047 TYR cc_start: 0.7405 (m-10) cc_final: 0.6975 (m-10) REVERT: E 54 ARG cc_start: 0.4913 (mmt-90) cc_final: 0.2723 (mtp180) REVERT: E 73 LEU cc_start: 0.6481 (tp) cc_final: 0.6057 (tp) REVERT: H 103 TRP cc_start: 0.7603 (m100) cc_final: 0.7122 (m-10) REVERT: L 21 ILE cc_start: 0.4876 (mm) cc_final: 0.4641 (mp) REVERT: L 31 TYR cc_start: 0.7454 (m-10) cc_final: 0.7187 (m-10) REVERT: L 49 TYR cc_start: 0.8285 (p90) cc_final: 0.7929 (p90) REVERT: L 96 TYR cc_start: 0.6125 (m-10) cc_final: 0.5870 (m-10) outliers start: 56 outliers final: 37 residues processed: 369 average time/residue: 0.1469 time to fit residues: 91.6792 Evaluate side-chains 338 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 229 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 762 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.158463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125417 restraints weight = 58942.977| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.54 r_work: 0.3639 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 26978 Z= 0.220 Angle : 0.679 10.161 36865 Z= 0.341 Chirality : 0.048 0.300 4329 Planarity : 0.005 0.056 4694 Dihedral : 6.718 59.583 4307 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer: Outliers : 2.75 % Allowed : 15.81 % Favored : 81.44 % 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: -1.79 (0.14), residues: 3339 helix: 0.10 (0.20), residues: 626 sheet: -1.41 (0.21), residues: 637 loop : -1.56 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 94 TYR 0.021 0.002 TYR B 453 PHE 0.023 0.002 PHE A 927 TRP 0.026 0.002 TRP B 104 HIS 0.011 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00503 (26907) covalent geometry : angle 0.65588 (36692) SS BOND : bond 0.00520 ( 37) SS BOND : angle 1.89488 ( 74) hydrogen bonds : bond 0.05028 ( 855) hydrogen bonds : angle 6.65780 ( 2259) Misc. bond : bond 0.00040 ( 1) link_BETA1-4 : bond 0.01021 ( 5) link_BETA1-4 : angle 3.27614 ( 15) link_BETA1-6 : bond 0.00374 ( 1) link_BETA1-6 : angle 2.44366 ( 3) link_NAG-ASN : bond 0.00463 ( 27) link_NAG-ASN : angle 3.08913 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 309 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7171 (mm) REVERT: A 275 PHE cc_start: 0.8299 (m-80) cc_final: 0.7924 (m-10) REVERT: A 592 PHE cc_start: 0.7280 (p90) cc_final: 0.6974 (p90) REVERT: A 973 ILE cc_start: 0.7114 (tp) cc_final: 0.6818 (tp) REVERT: A 1027 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.6778 (p) REVERT: A 1031 GLU cc_start: 0.7471 (tt0) cc_final: 0.7106 (pt0) REVERT: B 220 PHE cc_start: 0.7540 (p90) cc_final: 0.7072 (p90) REVERT: B 495 TYR cc_start: 0.5550 (t80) cc_final: 0.5216 (t80) REVERT: B 508 TYR cc_start: 0.7492 (m-10) cc_final: 0.7107 (m-10) REVERT: B 902 MET cc_start: 0.8081 (tpp) cc_final: 0.7750 (tpp) REVERT: B 988 GLU cc_start: 0.7837 (pm20) cc_final: 0.7458 (pm20) REVERT: C 104 TRP cc_start: 0.4963 (m-10) cc_final: 0.4634 (m-10) REVERT: C 280 ASN cc_start: 0.8679 (t0) cc_final: 0.8325 (t0) REVERT: C 347 PHE cc_start: 0.7913 (m-10) cc_final: 0.7486 (m-80) REVERT: E 32 ASP cc_start: 0.7365 (t70) cc_final: 0.6998 (t0) REVERT: E 73 LEU cc_start: 0.6649 (tp) cc_final: 0.6350 (tp) REVERT: H 103 TRP cc_start: 0.7620 (m100) cc_final: 0.7147 (m-10) REVERT: L 21 ILE cc_start: 0.4962 (mm) cc_final: 0.4717 (mp) REVERT: L 49 TYR cc_start: 0.8358 (p90) cc_final: 0.7767 (p90) outliers start: 77 outliers final: 54 residues processed: 358 average time/residue: 0.1382 time to fit residues: 85.1531 Evaluate side-chains 344 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 122 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 147 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1023 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.161254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128498 restraints weight = 58539.895| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.77 r_work: 0.3697 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26978 Z= 0.133 Angle : 0.614 10.632 36865 Z= 0.309 Chirality : 0.046 0.276 4329 Planarity : 0.004 0.055 4694 Dihedral : 6.467 59.983 4307 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 2.83 % Allowed : 16.88 % Favored : 80.29 % 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: -1.65 (0.14), residues: 3339 helix: 0.28 (0.21), residues: 628 sheet: -1.40 (0.21), residues: 617 loop : -1.47 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.025 0.001 TYR A 200 PHE 0.018 0.001 PHE B 318 TRP 0.017 0.001 TRP D 33 HIS 0.020 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00292 (26907) covalent geometry : angle 0.59225 (36692) SS BOND : bond 0.00436 ( 37) SS BOND : angle 1.70432 ( 74) hydrogen bonds : bond 0.04536 ( 855) hydrogen bonds : angle 6.36410 ( 2259) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.01107 ( 5) link_BETA1-4 : angle 3.17788 ( 15) link_BETA1-6 : bond 0.00487 ( 1) link_BETA1-6 : angle 2.51430 ( 3) link_NAG-ASN : bond 0.00635 ( 27) link_NAG-ASN : angle 2.81609 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 321 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7284 (mm) REVERT: A 275 PHE cc_start: 0.8254 (m-80) cc_final: 0.7866 (m-10) REVERT: A 592 PHE cc_start: 0.7271 (p90) cc_final: 0.6975 (p90) REVERT: A 726 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8710 (mm) REVERT: A 973 ILE cc_start: 0.6963 (tp) cc_final: 0.6653 (tp) REVERT: A 1027 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6814 (p) REVERT: A 1031 GLU cc_start: 0.7061 (tt0) cc_final: 0.6858 (pt0) REVERT: B 495 TYR cc_start: 0.5397 (t80) cc_final: 0.5069 (t80) REVERT: B 988 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: C 104 TRP cc_start: 0.4863 (m-10) cc_final: 0.4397 (m-10) REVERT: C 280 ASN cc_start: 0.8660 (t0) cc_final: 0.8306 (t0) REVERT: C 338 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7429 (t80) REVERT: C 347 PHE cc_start: 0.7761 (m-10) cc_final: 0.7434 (m-80) REVERT: D 92 CYS cc_start: 0.2406 (OUTLIER) cc_final: 0.1171 (p) REVERT: D 105 ARG cc_start: 0.4748 (ptt90) cc_final: 0.3934 (mmm160) REVERT: E 32 ASP cc_start: 0.7277 (t70) cc_final: 0.6860 (t0) REVERT: E 54 ARG cc_start: 0.4763 (mmt-90) cc_final: 0.2468 (mtp180) REVERT: E 73 LEU cc_start: 0.6770 (tp) cc_final: 0.6541 (tp) REVERT: H 103 TRP cc_start: 0.7555 (m100) cc_final: 0.7231 (m100) REVERT: L 21 ILE cc_start: 0.4927 (mm) cc_final: 0.4704 (mp) outliers start: 79 outliers final: 52 residues processed: 370 average time/residue: 0.1344 time to fit residues: 85.6287 Evaluate side-chains 343 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 25 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.160584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.126547 restraints weight = 58093.949| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.63 r_work: 0.3675 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26978 Z= 0.162 Angle : 0.626 9.888 36865 Z= 0.315 Chirality : 0.046 0.317 4329 Planarity : 0.004 0.052 4694 Dihedral : 6.441 59.810 4307 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.27 % Rotamer: Outliers : 3.04 % Allowed : 17.45 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3339 helix: 0.24 (0.20), residues: 628 sheet: -1.39 (0.21), residues: 625 loop : -1.50 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.034 0.001 TYR L 49 PHE 0.019 0.001 PHE B 592 TRP 0.018 0.002 TRP D 33 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00366 (26907) covalent geometry : angle 0.60225 (36692) SS BOND : bond 0.00644 ( 37) SS BOND : angle 2.06799 ( 74) hydrogen bonds : bond 0.04589 ( 855) hydrogen bonds : angle 6.28194 ( 2259) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.01118 ( 5) link_BETA1-4 : angle 3.14417 ( 15) link_BETA1-6 : bond 0.00435 ( 1) link_BETA1-6 : angle 2.46156 ( 3) link_NAG-ASN : bond 0.00449 ( 27) link_NAG-ASN : angle 2.84410 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 309 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7234 (mm) REVERT: A 275 PHE cc_start: 0.8279 (m-80) cc_final: 0.7862 (m-10) REVERT: A 592 PHE cc_start: 0.7343 (p90) cc_final: 0.7093 (p90) REVERT: A 726 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 973 ILE cc_start: 0.7007 (tp) cc_final: 0.6693 (tp) REVERT: A 1031 GLU cc_start: 0.7306 (tt0) cc_final: 0.6972 (pt0) REVERT: B 319 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7537 (tpp-160) REVERT: B 495 TYR cc_start: 0.5464 (t80) cc_final: 0.5096 (t80) REVERT: B 902 MET cc_start: 0.8162 (tpp) cc_final: 0.7846 (tpp) REVERT: B 988 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: C 104 TRP cc_start: 0.4852 (m-10) cc_final: 0.4355 (m-10) REVERT: C 280 ASN cc_start: 0.8659 (t0) cc_final: 0.8315 (t0) REVERT: C 338 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7657 (t80) REVERT: C 347 PHE cc_start: 0.7753 (m-10) cc_final: 0.7372 (m-80) REVERT: C 697 MET cc_start: 0.6139 (ttt) cc_final: 0.5857 (ttt) REVERT: D 92 CYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2209 (p) REVERT: E 32 ASP cc_start: 0.7283 (t70) cc_final: 0.6848 (t0) REVERT: H 56 ASP cc_start: 0.8468 (t0) cc_final: 0.7826 (p0) REVERT: H 103 TRP cc_start: 0.7614 (m100) cc_final: 0.7271 (m-10) REVERT: L 21 ILE cc_start: 0.5017 (mm) cc_final: 0.4787 (mp) REVERT: L 31 TYR cc_start: 0.7640 (m-10) cc_final: 0.7202 (m-10) REVERT: L 32 ASP cc_start: 0.8607 (m-30) cc_final: 0.7495 (t70) REVERT: L 49 TYR cc_start: 0.8332 (p90) cc_final: 0.8083 (p90) outliers start: 85 outliers final: 60 residues processed: 362 average time/residue: 0.1389 time to fit residues: 85.9884 Evaluate side-chains 358 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 299 optimal weight: 0.0570 chunk 255 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 0.0170 chunk 149 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 655 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.163560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129865 restraints weight = 58081.025| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.68 r_work: 0.3719 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26978 Z= 0.121 Angle : 0.608 10.860 36865 Z= 0.304 Chirality : 0.046 0.383 4329 Planarity : 0.004 0.060 4694 Dihedral : 6.245 58.439 4307 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 2.50 % Allowed : 18.06 % Favored : 79.43 % 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: -1.61 (0.15), residues: 3339 helix: 0.35 (0.20), residues: 633 sheet: -1.22 (0.21), residues: 662 loop : -1.52 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.030 0.001 TYR L 49 PHE 0.031 0.001 PHE B 194 TRP 0.023 0.002 TRP D 47 HIS 0.039 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00257 (26907) covalent geometry : angle 0.58650 (36692) SS BOND : bond 0.00640 ( 37) SS BOND : angle 1.94776 ( 74) hydrogen bonds : bond 0.04291 ( 855) hydrogen bonds : angle 6.06636 ( 2259) Misc. bond : bond 0.00020 ( 1) link_BETA1-4 : bond 0.01025 ( 5) link_BETA1-4 : angle 3.04919 ( 15) link_BETA1-6 : bond 0.00493 ( 1) link_BETA1-6 : angle 2.42645 ( 3) link_NAG-ASN : bond 0.00616 ( 27) link_NAG-ASN : angle 2.64095 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 328 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7106 (mm) REVERT: A 275 PHE cc_start: 0.8225 (m-80) cc_final: 0.7786 (m-10) REVERT: A 592 PHE cc_start: 0.7175 (p90) cc_final: 0.6940 (p90) REVERT: A 726 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 973 ILE cc_start: 0.6819 (tp) cc_final: 0.6518 (tp) REVERT: A 990 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8233 (mt-10) REVERT: A 1031 GLU cc_start: 0.6983 (tt0) cc_final: 0.6717 (pt0) REVERT: B 495 TYR cc_start: 0.5434 (t80) cc_final: 0.5063 (t80) REVERT: B 985 ASP cc_start: 0.7938 (p0) cc_final: 0.7711 (p0) REVERT: B 988 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: C 104 TRP cc_start: 0.4796 (m-10) cc_final: 0.4225 (m-10) REVERT: C 280 ASN cc_start: 0.8704 (t0) cc_final: 0.8348 (t0) REVERT: C 338 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7797 (t80) REVERT: C 347 PHE cc_start: 0.7705 (m-10) cc_final: 0.7412 (m-80) REVERT: C 463 PRO cc_start: 0.7850 (Cg_exo) cc_final: 0.7534 (Cg_endo) REVERT: C 568 ASP cc_start: 0.7687 (m-30) cc_final: 0.7359 (m-30) REVERT: C 697 MET cc_start: 0.6072 (ttt) cc_final: 0.5750 (ttt) REVERT: C 763 LEU cc_start: 0.9145 (mm) cc_final: 0.8759 (mm) REVERT: D 92 CYS cc_start: 0.2958 (OUTLIER) cc_final: 0.1843 (p) REVERT: D 105 ARG cc_start: 0.5031 (ptt90) cc_final: 0.4241 (mmm160) REVERT: E 32 ASP cc_start: 0.7241 (t70) cc_final: 0.6740 (t0) REVERT: H 56 ASP cc_start: 0.8451 (t0) cc_final: 0.7819 (p0) REVERT: H 103 TRP cc_start: 0.7612 (m100) cc_final: 0.7288 (m-10) REVERT: L 21 ILE cc_start: 0.4986 (mm) cc_final: 0.4553 (mp) REVERT: L 49 TYR cc_start: 0.8389 (p90) cc_final: 0.8178 (p90) outliers start: 70 outliers final: 50 residues processed: 377 average time/residue: 0.1421 time to fit residues: 92.1377 Evaluate side-chains 352 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 44 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 315 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN C 655 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.160635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.127337 restraints weight = 58724.414| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.82 r_work: 0.3662 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26978 Z= 0.181 Angle : 0.645 9.406 36865 Z= 0.323 Chirality : 0.047 0.289 4329 Planarity : 0.004 0.054 4694 Dihedral : 6.379 59.739 4307 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 2.86 % Allowed : 18.28 % Favored : 78.86 % 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: -1.72 (0.14), residues: 3339 helix: 0.18 (0.20), residues: 638 sheet: -1.29 (0.21), residues: 646 loop : -1.57 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.025 0.002 TYR L 49 PHE 0.059 0.002 PHE A 220 TRP 0.020 0.002 TRP D 36 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00413 (26907) covalent geometry : angle 0.62241 (36692) SS BOND : bond 0.00441 ( 37) SS BOND : angle 1.95598 ( 74) hydrogen bonds : bond 0.04645 ( 855) hydrogen bonds : angle 6.17371 ( 2259) Misc. bond : bond 0.00046 ( 1) link_BETA1-4 : bond 0.01035 ( 5) link_BETA1-4 : angle 3.07796 ( 15) link_BETA1-6 : bond 0.00259 ( 1) link_BETA1-6 : angle 3.31832 ( 3) link_NAG-ASN : bond 0.00585 ( 27) link_NAG-ASN : angle 2.81240 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 307 time to evaluate : 0.970 Fit side-chains REVERT: A 117 LEU cc_start: 0.5600 (mm) cc_final: 0.5334 (mt) REVERT: A 204 TYR cc_start: 0.5331 (m-80) cc_final: 0.4941 (m-80) REVERT: A 223 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7037 (mm) REVERT: A 275 PHE cc_start: 0.8286 (m-80) cc_final: 0.7842 (m-10) REVERT: A 592 PHE cc_start: 0.7217 (p90) cc_final: 0.6985 (p90) REVERT: A 726 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 973 ILE cc_start: 0.7025 (tp) cc_final: 0.6708 (tp) REVERT: A 1027 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 1031 GLU cc_start: 0.7312 (tt0) cc_final: 0.6940 (pt0) REVERT: B 495 TYR cc_start: 0.5443 (t80) cc_final: 0.5071 (t80) REVERT: B 900 MET cc_start: 0.7523 (mtp) cc_final: 0.7271 (mtp) REVERT: B 983 ARG cc_start: 0.8872 (tmt170) cc_final: 0.8401 (tpt90) REVERT: B 988 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: C 104 TRP cc_start: 0.5043 (m-10) cc_final: 0.4472 (m-10) REVERT: C 280 ASN cc_start: 0.8730 (t0) cc_final: 0.8359 (t0) REVERT: C 338 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7848 (t80) REVERT: C 347 PHE cc_start: 0.7800 (m-10) cc_final: 0.7341 (m-80) REVERT: C 463 PRO cc_start: 0.7984 (Cg_exo) cc_final: 0.7664 (Cg_endo) REVERT: C 697 MET cc_start: 0.6222 (ttt) cc_final: 0.5885 (ttt) REVERT: C 867 ASP cc_start: 0.8746 (t0) cc_final: 0.8506 (t0) REVERT: C 906 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: D 92 CYS cc_start: 0.3404 (OUTLIER) cc_final: 0.2307 (p) REVERT: E 32 ASP cc_start: 0.7377 (t70) cc_final: 0.6923 (t0) REVERT: H 56 ASP cc_start: 0.8494 (t0) cc_final: 0.7891 (p0) REVERT: H 103 TRP cc_start: 0.7633 (m100) cc_final: 0.7289 (m-10) REVERT: L 21 ILE cc_start: 0.5026 (mm) cc_final: 0.4809 (mp) REVERT: L 31 TYR cc_start: 0.7671 (m-10) cc_final: 0.7454 (m-80) REVERT: L 49 TYR cc_start: 0.8469 (p90) cc_final: 0.7972 (p90) outliers start: 80 outliers final: 63 residues processed: 355 average time/residue: 0.1427 time to fit residues: 86.0953 Evaluate side-chains 363 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 231 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 655 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126993 restraints weight = 58525.380| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.75 r_work: 0.3674 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26978 Z= 0.161 Angle : 0.633 9.505 36865 Z= 0.317 Chirality : 0.046 0.251 4329 Planarity : 0.004 0.057 4694 Dihedral : 6.326 59.516 4306 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 2.75 % Allowed : 18.60 % Favored : 78.65 % 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: -1.71 (0.14), residues: 3339 helix: 0.15 (0.20), residues: 639 sheet: -1.30 (0.21), residues: 649 loop : -1.55 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 105 TYR 0.024 0.001 TYR L 49 PHE 0.028 0.002 PHE A 220 TRP 0.024 0.002 TRP D 47 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00366 (26907) covalent geometry : angle 0.61082 (36692) SS BOND : bond 0.00365 ( 37) SS BOND : angle 1.78493 ( 74) hydrogen bonds : bond 0.04551 ( 855) hydrogen bonds : angle 6.09793 ( 2259) Misc. bond : bond 0.00038 ( 1) link_BETA1-4 : bond 0.01019 ( 5) link_BETA1-4 : angle 3.04005 ( 15) link_BETA1-6 : bond 0.00409 ( 1) link_BETA1-6 : angle 3.11054 ( 3) link_NAG-ASN : bond 0.00511 ( 27) link_NAG-ASN : angle 2.86020 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 301 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5685 (mm) cc_final: 0.5359 (mt) REVERT: A 204 TYR cc_start: 0.5362 (m-80) cc_final: 0.4218 (m-10) REVERT: A 223 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.5662 (mm) REVERT: A 275 PHE cc_start: 0.8258 (m-80) cc_final: 0.7868 (m-10) REVERT: A 592 PHE cc_start: 0.7207 (p90) cc_final: 0.6983 (p90) REVERT: A 726 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8664 (mm) REVERT: A 973 ILE cc_start: 0.7034 (tp) cc_final: 0.6714 (tp) REVERT: A 1027 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6723 (p) REVERT: A 1031 GLU cc_start: 0.7220 (tt0) cc_final: 0.6914 (pt0) REVERT: B 201 PHE cc_start: 0.7347 (t80) cc_final: 0.6964 (t80) REVERT: B 495 TYR cc_start: 0.5450 (t80) cc_final: 0.5093 (t80) REVERT: B 983 ARG cc_start: 0.8845 (tmt170) cc_final: 0.8402 (tpt90) REVERT: B 988 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: C 104 TRP cc_start: 0.5013 (m-10) cc_final: 0.4401 (m-10) REVERT: C 280 ASN cc_start: 0.8698 (t0) cc_final: 0.8403 (t0) REVERT: C 338 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7898 (t80) REVERT: C 347 PHE cc_start: 0.7835 (m-10) cc_final: 0.7398 (m-80) REVERT: C 463 PRO cc_start: 0.7946 (Cg_exo) cc_final: 0.7626 (Cg_endo) REVERT: C 574 ASP cc_start: 0.7591 (p0) cc_final: 0.7206 (p0) REVERT: C 697 MET cc_start: 0.6107 (ttt) cc_final: 0.5794 (ttt) REVERT: C 867 ASP cc_start: 0.8740 (t0) cc_final: 0.8505 (t0) REVERT: C 906 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7666 (m-10) REVERT: D 92 CYS cc_start: 0.3239 (OUTLIER) cc_final: 0.2274 (p) REVERT: D 105 ARG cc_start: 0.5279 (ptt90) cc_final: 0.4529 (mmm160) REVERT: E 32 ASP cc_start: 0.7409 (t70) cc_final: 0.6939 (t0) REVERT: H 56 ASP cc_start: 0.8533 (t0) cc_final: 0.7951 (p0) REVERT: H 103 TRP cc_start: 0.7641 (m100) cc_final: 0.7336 (m-10) REVERT: L 21 ILE cc_start: 0.4996 (mm) cc_final: 0.4551 (mp) REVERT: L 49 TYR cc_start: 0.8321 (p90) cc_final: 0.8101 (p90) outliers start: 77 outliers final: 61 residues processed: 350 average time/residue: 0.1369 time to fit residues: 82.0708 Evaluate side-chains 357 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 289 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.162833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129110 restraints weight = 58228.775| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.70 r_work: 0.3708 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26978 Z= 0.130 Angle : 0.617 10.414 36865 Z= 0.307 Chirality : 0.046 0.233 4329 Planarity : 0.004 0.061 4694 Dihedral : 6.151 58.047 4306 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 2.43 % Allowed : 19.06 % Favored : 78.51 % 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: -1.65 (0.14), residues: 3339 helix: 0.26 (0.20), residues: 638 sheet: -1.28 (0.21), residues: 655 loop : -1.51 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.022 0.001 TYR L 49 PHE 0.022 0.001 PHE C 275 TRP 0.027 0.002 TRP D 47 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00291 (26907) covalent geometry : angle 0.59807 (36692) SS BOND : bond 0.00310 ( 37) SS BOND : angle 1.63144 ( 74) hydrogen bonds : bond 0.04356 ( 855) hydrogen bonds : angle 5.94927 ( 2259) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.01035 ( 5) link_BETA1-4 : angle 2.98413 ( 15) link_BETA1-6 : bond 0.00376 ( 1) link_BETA1-6 : angle 2.80758 ( 3) link_NAG-ASN : bond 0.00546 ( 27) link_NAG-ASN : angle 2.66141 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 204 TYR cc_start: 0.5442 (m-80) cc_final: 0.4123 (m-10) REVERT: A 223 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.5638 (mm) REVERT: A 275 PHE cc_start: 0.8214 (m-80) cc_final: 0.7836 (m-10) REVERT: A 726 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 973 ILE cc_start: 0.6872 (tp) cc_final: 0.6544 (tp) REVERT: A 1027 THR cc_start: 0.7080 (OUTLIER) cc_final: 0.6665 (p) REVERT: B 201 PHE cc_start: 0.7314 (t80) cc_final: 0.6941 (t80) REVERT: B 495 TYR cc_start: 0.5383 (t80) cc_final: 0.5040 (t80) REVERT: B 900 MET cc_start: 0.7448 (mtp) cc_final: 0.7228 (mtp) REVERT: B 983 ARG cc_start: 0.8813 (tmt170) cc_final: 0.8377 (tpt90) REVERT: B 988 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: C 104 TRP cc_start: 0.4996 (m-10) cc_final: 0.4352 (m-10) REVERT: C 280 ASN cc_start: 0.8678 (t0) cc_final: 0.8399 (t0) REVERT: C 338 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.7952 (t80) REVERT: C 347 PHE cc_start: 0.7852 (m-10) cc_final: 0.7489 (m-80) REVERT: C 463 PRO cc_start: 0.7887 (Cg_exo) cc_final: 0.7564 (Cg_endo) REVERT: C 574 ASP cc_start: 0.7392 (p0) cc_final: 0.7034 (p0) REVERT: C 697 MET cc_start: 0.6081 (ttt) cc_final: 0.5772 (ttt) REVERT: C 763 LEU cc_start: 0.9069 (mm) cc_final: 0.8840 (mm) REVERT: C 906 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: C 916 LEU cc_start: 0.7936 (tp) cc_final: 0.7437 (tp) REVERT: D 92 CYS cc_start: 0.3266 (OUTLIER) cc_final: 0.2302 (p) REVERT: D 105 ARG cc_start: 0.5282 (ptt90) cc_final: 0.4478 (mmm160) REVERT: E 32 ASP cc_start: 0.7397 (t70) cc_final: 0.6917 (t0) REVERT: H 56 ASP cc_start: 0.8563 (t0) cc_final: 0.8041 (p0) REVERT: H 82 TRP cc_start: 0.6199 (m-90) cc_final: 0.4828 (m-90) REVERT: H 103 TRP cc_start: 0.7695 (m100) cc_final: 0.7419 (m-10) REVERT: L 21 ILE cc_start: 0.4987 (mm) cc_final: 0.4535 (mp) REVERT: L 49 TYR cc_start: 0.8333 (p90) cc_final: 0.7842 (p90) outliers start: 68 outliers final: 56 residues processed: 353 average time/residue: 0.1394 time to fit residues: 84.3986 Evaluate side-chains 353 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 64 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 78 optimal weight: 0.0980 chunk 281 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 chunk 187 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 919 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.163809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.130405 restraints weight = 58217.312| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.79 r_work: 0.3720 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26978 Z= 0.123 Angle : 0.612 9.718 36865 Z= 0.305 Chirality : 0.045 0.235 4329 Planarity : 0.004 0.064 4694 Dihedral : 6.018 57.588 4306 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.43 % Allowed : 19.13 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3339 helix: 0.32 (0.20), residues: 637 sheet: -1.19 (0.21), residues: 659 loop : -1.49 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.026 0.001 TYR L 49 PHE 0.023 0.001 PHE C 275 TRP 0.021 0.002 TRP D 47 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00273 (26907) covalent geometry : angle 0.59316 (36692) SS BOND : bond 0.00286 ( 37) SS BOND : angle 1.56227 ( 74) hydrogen bonds : bond 0.04273 ( 855) hydrogen bonds : angle 5.86381 ( 2259) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.01002 ( 5) link_BETA1-4 : angle 2.94949 ( 15) link_BETA1-6 : bond 0.00377 ( 1) link_BETA1-6 : angle 2.50246 ( 3) link_NAG-ASN : bond 0.00532 ( 27) link_NAG-ASN : angle 2.64050 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.08 seconds wall clock time: 118 minutes 57.62 seconds (7137.62 seconds total)