Starting phenix.real_space_refine on Fri Mar 6 08:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.cif Found real_map, /net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7knb_22941/03_2026/7knb_22941.map" } resolution = 3.93 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= 0.002 sd= 0.012 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 136 5.16 5 C 18616 2.51 5 N 4781 2.21 5 O 5691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 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: 29224 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7788 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 7772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7772 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8018 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.67, per 1000 atoms: 0.23 Number of scatterers: 29224 At special positions: 0 Unit cell: (134.366, 152.352, 224.296, 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 136 16.00 O 5691 8.00 N 4781 7.00 C 18616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.07 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 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=2.04 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 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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 B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 657 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 90 " " NAG D 706 " - " ASN D 53 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN B 717 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 43 sheets defined 31.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.605A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.023A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.516A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.994A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.662A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.762A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 762 Processing helix chain 'C' and resid 763 through 782 removed outlier: 3.624A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.612A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.044A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.545A 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 966 removed outlier: 4.330A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.217A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.696A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.237A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.991A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.250A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.695A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.288A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.867A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.892A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.742A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.885A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.947A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.663A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 942 removed outlier: 3.553A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.238A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.828A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.843A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.514A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.794A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.514A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.587A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.544A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.717A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.710A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.724A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.287A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.646A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.023A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.657A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.399A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.686A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.896A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.670A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.565A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.077A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.711A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.592A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.665A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 4.468A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.512A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 245 removed outlier: 3.950A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.662A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.769A pdb=" N LEU D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 267 " --> pdb=" O ALA D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.806A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.658A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.490A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.508A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.099A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.639A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.080A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.352A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.658A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 514 removed outlier: 3.874A pdb=" N ARG D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 514' Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.866A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 547 through 559 Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.754A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.046A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.771A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.080A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.380A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.565A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.510A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.741A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.596A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.399A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 703 through 704 removed outlier: 6.772A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.526A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1047 through 1051 removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.079A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.640A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1086 through 1088 removed outlier: 3.512A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.277A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.085A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 323 through 328 removed outlier: 4.852A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.854A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AC6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AC7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.698A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.698A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1086 through 1088 removed outlier: 3.720A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.785A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.539A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.860A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.871A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD9, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.536A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.826A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.826A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.308A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.509A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2802 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: 7.02 Time building geometry restraints manager: 3.15 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: 9292 1.34 - 1.47: 7464 1.47 - 1.59: 12950 1.59 - 1.72: 0 1.72 - 1.84: 183 Bond restraints: 29889 Sorted by residual: bond pdb=" N ASP A 994 " pdb=" CA ASP A 994 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.35e+00 bond pdb=" N LEU A 752 " pdb=" CA LEU A 752 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.61e+00 bond pdb=" N SER A 940 " pdb=" CA SER A 940 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.55e+00 bond pdb=" N THR A 941 " pdb=" CA THR A 941 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.34e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 29884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 39598 1.48 - 2.95: 842 2.95 - 4.43: 204 4.43 - 5.91: 22 5.91 - 7.39: 5 Bond angle restraints: 40671 Sorted by residual: angle pdb=" CA TYR A 756 " pdb=" C TYR A 756 " pdb=" O TYR A 756 " ideal model delta sigma weight residual 120.55 116.48 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" CA THR A 941 " pdb=" C THR A 941 " pdb=" O THR A 941 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.43e+01 angle pdb=" C TYR A 756 " pdb=" CA TYR A 756 " pdb=" CB TYR A 756 " ideal model delta sigma weight residual 110.79 116.71 -5.92 1.66e+00 3.63e-01 1.27e+01 angle pdb=" N ALA A 944 " pdb=" CA ALA A 944 " pdb=" C ALA A 944 " ideal model delta sigma weight residual 113.16 108.82 4.34 1.24e+00 6.50e-01 1.22e+01 angle pdb=" CA SER A 943 " pdb=" C SER A 943 " pdb=" O SER A 943 " ideal model delta sigma weight residual 121.54 117.71 3.83 1.16e+00 7.43e-01 1.09e+01 ... (remaining 40666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16699 17.93 - 35.86: 1434 35.86 - 53.78: 272 53.78 - 71.71: 74 71.71 - 89.64: 29 Dihedral angle restraints: 18508 sinusoidal: 7910 harmonic: 10598 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 22.47 70.53 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 151.36 -58.36 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 18505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4109 0.061 - 0.123: 594 0.123 - 0.184: 38 0.184 - 0.246: 2 0.246 - 0.307: 5 Chirality restraints: 4748 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 432 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 4745 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO B 337 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 987 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO A 272 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.030 5.00e-02 4.00e+02 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2951 2.75 - 3.28: 30328 3.28 - 3.82: 47286 3.82 - 4.36: 55587 4.36 - 4.90: 93773 Nonbonded interactions: 229925 Sorted by model distance: nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 659 " pdb=" O THR A 696 " model vdw 2.213 3.040 nonbonded pdb=" N LYS C 187 " pdb=" O ILE C 210 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP D 67 " pdb=" N LYS D 68 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 929 " pdb=" NZ LYS B 933 " model vdw 2.227 3.120 ... (remaining 229920 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 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 62 \ 0 or resid 640 through 676 or resid 690 through 1313)) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 139 or (resid 140 through 141 and (name N or name CA or name \ C or name O or name CB )) or (resid 156 and (name N or name CA or name C or name \ O or name CB )) or resid 157 through 158 or (resid 159 through 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 174 throug \ h 176 or (resid 187 through 188 and (name N or name CA or name C or name O or na \ me CB )) or resid 189 through 194 or (resid 195 through 198 and (name N or name \ CA or name C or name O or name CB )) or resid 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 243 or resid 264 t \ hrough 280 or (resid 281 and (name N or name CA or name C or name O or name CB ) \ ) or resid 282 through 620 or resid 640 through 811 or resid 815 through 828 or \ resid 853 through 1146 or resid 1302 through 1314)) selection = (chain 'C' and (resid 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 13 \ 4 or (resid 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 189 or (resid 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB )) or resid 291 through 620 or resid 640 through 676 or re \ sid 690 through 1313)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue 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: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.990 Find NCS groups from input model: 0.710 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.003 0.046 29987 Z= 0.164 Angle : 0.560 7.386 40923 Z= 0.292 Chirality : 0.044 0.307 4748 Planarity : 0.003 0.074 5193 Dihedral : 13.766 89.639 11550 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3583 helix: -0.03 (0.18), residues: 894 sheet: 0.11 (0.22), residues: 617 loop : -0.69 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 177 TYR 0.026 0.001 TYR D 217 PHE 0.007 0.001 PHE B 338 TRP 0.022 0.001 TRP D 271 HIS 0.006 0.000 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00323 (29889) covalent geometry : angle 0.55137 (40671) SS BOND : bond 0.00690 ( 42) SS BOND : angle 0.83936 ( 84) hydrogen bonds : bond 0.29076 ( 970) hydrogen bonds : angle 9.53371 ( 2802) link_BETA1-4 : bond 0.00253 ( 5) link_BETA1-4 : angle 0.96218 ( 15) link_NAG-ASN : bond 0.00392 ( 51) link_NAG-ASN : angle 1.61686 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8900 (mpp) cc_final: 0.8555 (mpp) REVERT: A 1050 MET cc_start: 0.8677 (pmm) cc_final: 0.8359 (pmm) REVERT: B 731 MET cc_start: 0.8142 (ptm) cc_final: 0.7801 (ptm) REVERT: B 1050 MET cc_start: 0.8877 (pmm) cc_final: 0.8393 (pmm) REVERT: D 270 MET cc_start: 0.5474 (tmm) cc_final: 0.4634 (tmm) REVERT: D 480 MET cc_start: -0.1051 (ppp) cc_final: -0.1273 (ppp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1530 time to fit residues: 23.1588 Evaluate side-chains 71 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN C1036 GLN B 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.037484 restraints weight = 306391.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.038388 restraints weight = 168160.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.038947 restraints weight = 109503.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.039255 restraints weight = 81105.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.039604 restraints weight = 66742.587| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29987 Z= 0.121 Angle : 0.566 9.594 40923 Z= 0.292 Chirality : 0.046 0.370 4748 Planarity : 0.004 0.052 5193 Dihedral : 6.478 56.237 5058 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3583 helix: 0.39 (0.17), residues: 957 sheet: 0.08 (0.21), residues: 608 loop : -0.71 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.013 0.001 TYR C 756 PHE 0.015 0.001 PHE B 329 TRP 0.016 0.001 TRP D 477 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00248 (29889) covalent geometry : angle 0.55166 (40671) SS BOND : bond 0.00191 ( 42) SS BOND : angle 0.85557 ( 84) hydrogen bonds : bond 0.05553 ( 970) hydrogen bonds : angle 6.46820 ( 2802) link_BETA1-4 : bond 0.00529 ( 5) link_BETA1-4 : angle 0.83280 ( 15) link_NAG-ASN : bond 0.00542 ( 51) link_NAG-ASN : angle 2.04422 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.8265 (ppp) cc_final: 0.8047 (ppp) REVERT: C 1050 MET cc_start: 0.8989 (pmm) cc_final: 0.8288 (pmm) REVERT: A 869 MET cc_start: 0.9197 (pmm) cc_final: 0.8923 (pmm) REVERT: A 900 MET cc_start: 0.9129 (mpp) cc_final: 0.8892 (mpp) REVERT: A 1050 MET cc_start: 0.8965 (pmm) cc_final: 0.8743 (pmm) REVERT: B 697 MET cc_start: 0.8932 (mmm) cc_final: 0.8457 (mmp) REVERT: B 731 MET cc_start: 0.8769 (ptm) cc_final: 0.8313 (ptm) REVERT: B 1050 MET cc_start: 0.9049 (pmm) cc_final: 0.8530 (pmm) REVERT: D 82 MET cc_start: 0.6342 (ppp) cc_final: 0.5624 (pmm) REVERT: D 323 MET cc_start: 0.1554 (tpp) cc_final: 0.1289 (tpp) REVERT: D 383 MET cc_start: 0.8355 (mpp) cc_final: 0.8035 (pmm) REVERT: D 462 MET cc_start: 0.4217 (pmm) cc_final: 0.4006 (pmm) REVERT: D 480 MET cc_start: -0.0366 (ppp) cc_final: -0.0613 (ppp) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.1609 time to fit residues: 24.8892 Evaluate side-chains 77 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 159 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 351 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 334 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 87 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN C1083 HIS A 388 ASN A1071 GLN A1083 HIS B 644 GLN B 751 ASN B1083 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.053055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.034215 restraints weight = 284496.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.034440 restraints weight = 167703.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.034923 restraints weight = 114144.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.035266 restraints weight = 85581.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.035388 restraints weight = 69714.326| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29987 Z= 0.173 Angle : 0.565 9.263 40923 Z= 0.289 Chirality : 0.044 0.363 4748 Planarity : 0.004 0.051 5193 Dihedral : 5.752 57.248 5058 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.61 % Allowed : 7.74 % Favored : 91.65 % 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: -0.46 (0.14), residues: 3583 helix: 0.56 (0.17), residues: 979 sheet: -0.11 (0.21), residues: 598 loop : -0.77 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 765 TYR 0.013 0.001 TYR A 904 PHE 0.017 0.001 PHE B 392 TRP 0.015 0.001 TRP D 48 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00362 (29889) covalent geometry : angle 0.54903 (40671) SS BOND : bond 0.00382 ( 42) SS BOND : angle 0.96764 ( 84) hydrogen bonds : bond 0.04358 ( 970) hydrogen bonds : angle 5.78434 ( 2802) link_BETA1-4 : bond 0.00318 ( 5) link_BETA1-4 : angle 1.18018 ( 15) link_NAG-ASN : bond 0.00476 ( 51) link_NAG-ASN : angle 2.17030 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: C 1050 MET cc_start: 0.9017 (pmm) cc_final: 0.8424 (pmm) REVERT: C 1122 VAL cc_start: 0.9589 (OUTLIER) cc_final: 0.9388 (t) REVERT: A 388 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7570 (p0) REVERT: A 900 MET cc_start: 0.9320 (mpp) cc_final: 0.8363 (mmp) REVERT: A 1050 MET cc_start: 0.9095 (pmm) cc_final: 0.8798 (pmm) REVERT: B 517 LEU cc_start: 0.8386 (tp) cc_final: 0.8180 (tp) REVERT: B 697 MET cc_start: 0.8994 (mmm) cc_final: 0.8652 (mmp) REVERT: B 731 MET cc_start: 0.8933 (ptm) cc_final: 0.8459 (ptm) REVERT: B 900 MET cc_start: 0.8947 (pmm) cc_final: 0.8714 (pmm) REVERT: B 1001 LEU cc_start: 0.9805 (tp) cc_final: 0.9571 (pp) REVERT: B 1010 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: B 1050 MET cc_start: 0.9110 (pmm) cc_final: 0.8616 (pmm) REVERT: D 152 MET cc_start: -0.2923 (tpp) cc_final: -0.3159 (tmm) REVERT: D 323 MET cc_start: 0.2944 (tpp) cc_final: 0.2707 (tpp) REVERT: D 480 MET cc_start: 0.1101 (ppp) cc_final: 0.0829 (ppp) REVERT: D 581 VAL cc_start: -0.3943 (OUTLIER) cc_final: -0.4199 (m) outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 0.1646 time to fit residues: 28.0929 Evaluate side-chains 86 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 18 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 220 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 59 optimal weight: 0.4980 chunk 347 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN A 388 ASN A 935 GLN A1036 GLN B 52 GLN B1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.051593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033654 restraints weight = 302823.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.033920 restraints weight = 166381.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.034310 restraints weight = 108805.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034443 restraints weight = 81993.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034667 restraints weight = 71065.858| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29987 Z= 0.179 Angle : 0.559 9.319 40923 Z= 0.285 Chirality : 0.044 0.365 4748 Planarity : 0.004 0.054 5193 Dihedral : 5.582 57.473 5058 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.92 % Allowed : 9.50 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3583 helix: 0.74 (0.17), residues: 970 sheet: -0.30 (0.21), residues: 592 loop : -0.78 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 765 TYR 0.011 0.001 TYR B1067 PHE 0.014 0.001 PHE A 306 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00373 (29889) covalent geometry : angle 0.54271 (40671) SS BOND : bond 0.00330 ( 42) SS BOND : angle 0.91212 ( 84) hydrogen bonds : bond 0.03841 ( 970) hydrogen bonds : angle 5.61759 ( 2802) link_BETA1-4 : bond 0.00170 ( 5) link_BETA1-4 : angle 1.15205 ( 15) link_NAG-ASN : bond 0.00472 ( 51) link_NAG-ASN : angle 2.19254 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9237 (tpp) cc_final: 0.8921 (mtt) REVERT: A 900 MET cc_start: 0.9403 (mpp) cc_final: 0.8540 (mmp) REVERT: A 1050 MET cc_start: 0.9139 (pmm) cc_final: 0.8808 (pmm) REVERT: B 697 MET cc_start: 0.8992 (mmm) cc_final: 0.8672 (mmp) REVERT: B 731 MET cc_start: 0.8951 (ptm) cc_final: 0.8431 (ptm) REVERT: B 740 MET cc_start: 0.7555 (ppp) cc_final: 0.7315 (ppp) REVERT: B 943 SER cc_start: 0.8719 (m) cc_final: 0.8271 (t) REVERT: B 1001 LEU cc_start: 0.9812 (tp) cc_final: 0.9573 (pp) REVERT: B 1010 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8877 (pm20) REVERT: B 1050 MET cc_start: 0.9163 (pmm) cc_final: 0.8572 (pmm) REVERT: D 152 MET cc_start: -0.4011 (tpp) cc_final: -0.4317 (tmm) REVERT: D 249 MET cc_start: 0.0019 (mmp) cc_final: -0.0190 (mmp) REVERT: D 323 MET cc_start: 0.5249 (tpp) cc_final: 0.4819 (tpp) REVERT: D 480 MET cc_start: 0.1871 (ppp) cc_final: 0.1609 (ppp) outliers start: 29 outliers final: 18 residues processed: 102 average time/residue: 0.1537 time to fit residues: 27.9552 Evaluate side-chains 90 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1083 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 56 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 333 optimal weight: 0.4980 chunk 201 optimal weight: 0.4980 chunk 314 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 804 GLN B1083 HIS ** D 58 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.051582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.033995 restraints weight = 300916.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.034700 restraints weight = 175931.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034849 restraints weight = 106837.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.035015 restraints weight = 70326.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.035023 restraints weight = 65097.242| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29987 Z= 0.144 Angle : 0.532 9.388 40923 Z= 0.269 Chirality : 0.044 0.357 4748 Planarity : 0.004 0.055 5193 Dihedral : 5.431 57.672 5058 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.12 % Allowed : 10.42 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3583 helix: 0.82 (0.17), residues: 980 sheet: -0.33 (0.21), residues: 591 loop : -0.81 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1019 TYR 0.011 0.001 TYR B1067 PHE 0.016 0.001 PHE C 392 TRP 0.011 0.001 TRP D 168 HIS 0.022 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00302 (29889) covalent geometry : angle 0.51478 (40671) SS BOND : bond 0.00333 ( 42) SS BOND : angle 0.90442 ( 84) hydrogen bonds : bond 0.03570 ( 970) hydrogen bonds : angle 5.40964 ( 2802) link_BETA1-4 : bond 0.00191 ( 5) link_BETA1-4 : angle 1.12201 ( 15) link_NAG-ASN : bond 0.00463 ( 51) link_NAG-ASN : angle 2.16804 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1122 VAL cc_start: 0.9562 (OUTLIER) cc_final: 0.9328 (t) REVERT: A 388 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7932 (p0) REVERT: A 731 MET cc_start: 0.8931 (ppp) cc_final: 0.8568 (ppp) REVERT: A 740 MET cc_start: 0.9177 (tpp) cc_final: 0.8853 (mtt) REVERT: A 900 MET cc_start: 0.9398 (mpp) cc_final: 0.8561 (mmp) REVERT: A 1050 MET cc_start: 0.9114 (pmm) cc_final: 0.8796 (pmm) REVERT: B 731 MET cc_start: 0.8876 (ptm) cc_final: 0.8274 (ptm) REVERT: B 943 SER cc_start: 0.8701 (m) cc_final: 0.8258 (t) REVERT: B 979 ASP cc_start: 0.9467 (m-30) cc_final: 0.9266 (t0) REVERT: B 1001 LEU cc_start: 0.9806 (tp) cc_final: 0.9568 (pp) REVERT: B 1010 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: B 1050 MET cc_start: 0.9101 (pmm) cc_final: 0.8512 (pmm) REVERT: D 152 MET cc_start: -0.3674 (tpp) cc_final: -0.4211 (tmm) REVERT: D 581 VAL cc_start: -0.4108 (OUTLIER) cc_final: -0.4354 (m) outliers start: 35 outliers final: 19 residues processed: 104 average time/residue: 0.1498 time to fit residues: 27.9835 Evaluate side-chains 94 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 325 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** D 58 ASN ** 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 = 0.3649 r_free = 0.3649 target = 0.051623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033511 restraints weight = 301890.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033996 restraints weight = 163773.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.034349 restraints weight = 108551.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034501 restraints weight = 81421.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.034671 restraints weight = 69113.042| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29987 Z= 0.125 Angle : 0.528 10.860 40923 Z= 0.264 Chirality : 0.044 0.351 4748 Planarity : 0.004 0.057 5193 Dihedral : 5.314 57.798 5058 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.24 % Allowed : 11.25 % Favored : 87.51 % 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: -0.40 (0.14), residues: 3583 helix: 0.88 (0.17), residues: 983 sheet: -0.29 (0.21), residues: 587 loop : -0.82 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.012 0.001 TYR B1067 PHE 0.017 0.001 PHE C 392 TRP 0.011 0.001 TRP D 168 HIS 0.007 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00265 (29889) covalent geometry : angle 0.51068 (40671) SS BOND : bond 0.00261 ( 42) SS BOND : angle 0.89113 ( 84) hydrogen bonds : bond 0.03400 ( 970) hydrogen bonds : angle 5.29372 ( 2802) link_BETA1-4 : bond 0.00175 ( 5) link_BETA1-4 : angle 1.05420 ( 15) link_NAG-ASN : bond 0.00462 ( 51) link_NAG-ASN : angle 2.14085 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: C 753 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9057 (mm) REVERT: C 1122 VAL cc_start: 0.9556 (OUTLIER) cc_final: 0.9309 (t) REVERT: A 740 MET cc_start: 0.9225 (tpp) cc_final: 0.8864 (mtt) REVERT: A 900 MET cc_start: 0.9440 (mpp) cc_final: 0.8705 (mmt) REVERT: A 1050 MET cc_start: 0.9172 (pmm) cc_final: 0.8820 (pmm) REVERT: B 697 MET cc_start: 0.8905 (mmm) cc_final: 0.8289 (mmm) REVERT: B 731 MET cc_start: 0.8920 (ptm) cc_final: 0.8475 (ptm) REVERT: B 900 MET cc_start: 0.9150 (pmm) cc_final: 0.8564 (pmm) REVERT: B 943 SER cc_start: 0.8702 (m) cc_final: 0.8205 (t) REVERT: B 1001 LEU cc_start: 0.9814 (tp) cc_final: 0.9584 (pp) REVERT: B 1010 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8950 (pm20) REVERT: B 1050 MET cc_start: 0.9059 (pmm) cc_final: 0.8446 (pmm) REVERT: D 152 MET cc_start: -0.3626 (tpp) cc_final: -0.4007 (tmm) outliers start: 39 outliers final: 24 residues processed: 109 average time/residue: 0.1506 time to fit residues: 29.8361 Evaluate side-chains 95 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 200 optimal weight: 10.0000 chunk 172 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 358 optimal weight: 20.0000 chunk 310 optimal weight: 40.0000 chunk 292 optimal weight: 0.1980 chunk 242 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.051243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.033529 restraints weight = 302926.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.033692 restraints weight = 167498.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034114 restraints weight = 111636.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.034263 restraints weight = 81590.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.034486 restraints weight = 69169.156| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29987 Z= 0.148 Angle : 0.546 9.434 40923 Z= 0.275 Chirality : 0.044 0.349 4748 Planarity : 0.004 0.056 5193 Dihedral : 5.213 58.007 5058 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.34 % Allowed : 11.89 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3583 helix: 0.92 (0.17), residues: 991 sheet: -0.33 (0.21), residues: 580 loop : -0.84 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 457 TYR 0.011 0.001 TYR B1067 PHE 0.009 0.001 PHE B 329 TRP 0.011 0.001 TRP D 168 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00313 (29889) covalent geometry : angle 0.52945 (40671) SS BOND : bond 0.00293 ( 42) SS BOND : angle 0.96439 ( 84) hydrogen bonds : bond 0.03348 ( 970) hydrogen bonds : angle 5.23600 ( 2802) link_BETA1-4 : bond 0.00415 ( 5) link_BETA1-4 : angle 1.15135 ( 15) link_NAG-ASN : bond 0.00457 ( 51) link_NAG-ASN : angle 2.16279 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: C 753 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 740 MET cc_start: 0.9161 (tpp) cc_final: 0.8835 (mtt) REVERT: A 869 MET cc_start: 0.9325 (pmm) cc_final: 0.9119 (pmm) REVERT: A 900 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8777 (mmt) REVERT: A 1050 MET cc_start: 0.9196 (pmm) cc_final: 0.8844 (pmm) REVERT: B 697 MET cc_start: 0.8858 (mmm) cc_final: 0.8325 (mmm) REVERT: B 731 MET cc_start: 0.8874 (ptm) cc_final: 0.8416 (ptm) REVERT: B 900 MET cc_start: 0.9188 (pmm) cc_final: 0.8554 (pmm) REVERT: B 943 SER cc_start: 0.8836 (m) cc_final: 0.8354 (t) REVERT: B 1001 LEU cc_start: 0.9803 (tp) cc_final: 0.9584 (pp) REVERT: B 1010 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: B 1050 MET cc_start: 0.9060 (pmm) cc_final: 0.8506 (pmm) REVERT: D 581 VAL cc_start: -0.3590 (OUTLIER) cc_final: -0.3831 (m) outliers start: 42 outliers final: 28 residues processed: 109 average time/residue: 0.1489 time to fit residues: 29.3860 Evaluate side-chains 101 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 288 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 333 optimal weight: 30.0000 chunk 281 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.051376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.033614 restraints weight = 302011.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034297 restraints weight = 167926.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.034547 restraints weight = 101077.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034722 restraints weight = 77269.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.034826 restraints weight = 65352.945| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29987 Z= 0.120 Angle : 0.533 9.473 40923 Z= 0.265 Chirality : 0.044 0.343 4748 Planarity : 0.004 0.057 5193 Dihedral : 5.107 58.013 5058 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.24 % Allowed : 12.52 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3583 helix: 1.00 (0.17), residues: 989 sheet: -0.32 (0.21), residues: 573 loop : -0.85 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1019 TYR 0.012 0.001 TYR B1067 PHE 0.014 0.001 PHE A 306 TRP 0.011 0.001 TRP D 168 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00255 (29889) covalent geometry : angle 0.51647 (40671) SS BOND : bond 0.00378 ( 42) SS BOND : angle 0.89771 ( 84) hydrogen bonds : bond 0.03208 ( 970) hydrogen bonds : angle 5.11683 ( 2802) link_BETA1-4 : bond 0.00174 ( 5) link_BETA1-4 : angle 1.02340 ( 15) link_NAG-ASN : bond 0.00459 ( 51) link_NAG-ASN : angle 2.13120 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: C 392 PHE cc_start: 0.8071 (t80) cc_final: 0.7698 (t80) REVERT: C 753 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9149 (mm) REVERT: A 740 MET cc_start: 0.9146 (tpp) cc_final: 0.8817 (mtt) REVERT: A 869 MET cc_start: 0.9324 (pmm) cc_final: 0.9118 (pmm) REVERT: A 900 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8721 (mmt) REVERT: A 1050 MET cc_start: 0.9176 (pmm) cc_final: 0.8839 (pmm) REVERT: B 210 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B 697 MET cc_start: 0.8857 (mmm) cc_final: 0.8389 (mmm) REVERT: B 731 MET cc_start: 0.8785 (ptm) cc_final: 0.8335 (ptm) REVERT: B 943 SER cc_start: 0.8793 (m) cc_final: 0.8222 (t) REVERT: B 1001 LEU cc_start: 0.9805 (tp) cc_final: 0.9584 (pp) REVERT: B 1010 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: B 1050 MET cc_start: 0.9089 (pmm) cc_final: 0.8402 (pmm) REVERT: D 152 MET cc_start: -0.3273 (tpp) cc_final: -0.3796 (tmm) REVERT: D 581 VAL cc_start: -0.3688 (OUTLIER) cc_final: -0.3942 (m) outliers start: 39 outliers final: 29 residues processed: 109 average time/residue: 0.1496 time to fit residues: 29.6106 Evaluate side-chains 105 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 166 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 169 optimal weight: 0.0170 chunk 140 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.051190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.033419 restraints weight = 301653.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033818 restraints weight = 166124.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034223 restraints weight = 106644.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.034544 restraints weight = 78604.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034603 restraints weight = 64459.294| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29987 Z= 0.125 Angle : 0.545 12.532 40923 Z= 0.271 Chirality : 0.044 0.344 4748 Planarity : 0.003 0.056 5193 Dihedral : 5.037 58.126 5058 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.24 % Allowed : 12.94 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3583 helix: 1.05 (0.17), residues: 989 sheet: -0.32 (0.21), residues: 586 loop : -0.84 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.011 0.001 TYR B1067 PHE 0.009 0.001 PHE B 329 TRP 0.011 0.001 TRP D 168 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00267 (29889) covalent geometry : angle 0.52900 (40671) SS BOND : bond 0.00272 ( 42) SS BOND : angle 0.87649 ( 84) hydrogen bonds : bond 0.03212 ( 970) hydrogen bonds : angle 5.08149 ( 2802) link_BETA1-4 : bond 0.00198 ( 5) link_BETA1-4 : angle 1.07050 ( 15) link_NAG-ASN : bond 0.00456 ( 51) link_NAG-ASN : angle 2.13834 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 753 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9103 (mm) REVERT: A 740 MET cc_start: 0.9169 (tpp) cc_final: 0.8834 (mtt) REVERT: A 869 MET cc_start: 0.9333 (pmm) cc_final: 0.9128 (pmm) REVERT: A 900 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8752 (mmt) REVERT: A 1050 MET cc_start: 0.9174 (pmm) cc_final: 0.8774 (pmm) REVERT: B 210 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 697 MET cc_start: 0.8885 (mmm) cc_final: 0.8457 (mmm) REVERT: B 731 MET cc_start: 0.8815 (ptm) cc_final: 0.8390 (ptm) REVERT: B 943 SER cc_start: 0.8803 (m) cc_final: 0.8231 (t) REVERT: B 1001 LEU cc_start: 0.9809 (tp) cc_final: 0.9589 (pp) REVERT: B 1010 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (pm20) REVERT: B 1050 MET cc_start: 0.9050 (pmm) cc_final: 0.8513 (pmm) REVERT: D 152 MET cc_start: -0.3357 (tpp) cc_final: -0.3709 (tmm) REVERT: D 581 VAL cc_start: -0.3581 (OUTLIER) cc_final: -0.3833 (m) outliers start: 39 outliers final: 30 residues processed: 106 average time/residue: 0.1447 time to fit residues: 27.8050 Evaluate side-chains 104 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 112 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 279 optimal weight: 0.0970 chunk 139 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 360 optimal weight: 8.9990 chunk 266 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1108 ASN D 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.051307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.033486 restraints weight = 299737.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033636 restraints weight = 163771.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.034066 restraints weight = 107676.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.034368 restraints weight = 81174.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.034450 restraints weight = 65422.150| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29987 Z= 0.109 Angle : 0.534 11.508 40923 Z= 0.264 Chirality : 0.044 0.339 4748 Planarity : 0.004 0.057 5193 Dihedral : 4.961 58.206 5058 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 13.00 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3583 helix: 1.08 (0.17), residues: 997 sheet: -0.37 (0.20), residues: 605 loop : -0.82 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.012 0.001 TYR B1067 PHE 0.016 0.001 PHE A 306 TRP 0.011 0.001 TRP D 168 HIS 0.002 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00234 (29889) covalent geometry : angle 0.51823 (40671) SS BOND : bond 0.00240 ( 42) SS BOND : angle 0.82635 ( 84) hydrogen bonds : bond 0.03126 ( 970) hydrogen bonds : angle 4.98643 ( 2802) link_BETA1-4 : bond 0.00169 ( 5) link_BETA1-4 : angle 0.99513 ( 15) link_NAG-ASN : bond 0.00461 ( 51) link_NAG-ASN : angle 2.11090 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: C 753 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9103 (mm) REVERT: A 740 MET cc_start: 0.9209 (tpp) cc_final: 0.8877 (mtt) REVERT: A 869 MET cc_start: 0.9348 (pmm) cc_final: 0.9141 (pmm) REVERT: A 900 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9060 (mpp) REVERT: A 1050 MET cc_start: 0.9209 (pmm) cc_final: 0.8782 (pmm) REVERT: B 210 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 697 MET cc_start: 0.8883 (mmm) cc_final: 0.8447 (mmm) REVERT: B 731 MET cc_start: 0.8834 (ptm) cc_final: 0.8424 (ptm) REVERT: B 943 SER cc_start: 0.8867 (m) cc_final: 0.8298 (t) REVERT: B 1001 LEU cc_start: 0.9824 (tp) cc_final: 0.9589 (pp) REVERT: B 1010 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: B 1050 MET cc_start: 0.9022 (pmm) cc_final: 0.8497 (pmm) REVERT: D 152 MET cc_start: -0.3763 (tpp) cc_final: -0.4097 (tmm) outliers start: 35 outliers final: 29 residues processed: 104 average time/residue: 0.1517 time to fit residues: 28.9126 Evaluate side-chains 101 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 98 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 315 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 310 optimal weight: 7.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN D 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.050502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.032782 restraints weight = 302215.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.032881 restraints weight = 172721.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033303 restraints weight = 111306.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033634 restraints weight = 79835.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033721 restraints weight = 63454.719| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29987 Z= 0.154 Angle : 0.566 11.415 40923 Z= 0.282 Chirality : 0.044 0.342 4748 Planarity : 0.004 0.055 5193 Dihedral : 5.074 58.833 5058 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.21 % Allowed : 12.94 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3583 helix: 1.06 (0.17), residues: 993 sheet: -0.37 (0.20), residues: 604 loop : -0.84 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.013 0.001 TYR A 269 PHE 0.011 0.001 PHE C 168 TRP 0.017 0.001 TRP C 64 HIS 0.018 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00325 (29889) covalent geometry : angle 0.54957 (40671) SS BOND : bond 0.00307 ( 42) SS BOND : angle 0.91470 ( 84) hydrogen bonds : bond 0.03270 ( 970) hydrogen bonds : angle 5.11809 ( 2802) link_BETA1-4 : bond 0.00174 ( 5) link_BETA1-4 : angle 1.16177 ( 15) link_NAG-ASN : bond 0.00461 ( 51) link_NAG-ASN : angle 2.21280 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.16 seconds wall clock time: 96 minutes 42.67 seconds (5802.67 seconds total)