Starting phenix.real_space_refine on Thu Mar 5 16:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.map" model { file = "/net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tat_25784/03_2026/7tat_25784.cif" } resolution = 3.2 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= 0.064 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 110 5.16 5 C 15184 2.51 5 N 4138 2.21 5 O 4494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.02s 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: 23926 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 6961 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 926} Chain breaks: 11 Unresolved non-hydrogen bonds: 716 Unresolved non-hydrogen angles: 896 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 30, 'ASN:plan1': 19, 'GLU:plan': 21, 'ARG:plan': 11, 'GLN:plan1': 14, 'PHE:plan': 7, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 431 Chain: "B" Number of atoms: 6518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 6518 Classifications: {'peptide': 956} Incomplete info: {'truncation_to_alanine': 306} Link IDs: {'PTRANS': 52, 'TRANS': 903} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 978 Unresolved non-hydrogen angles: 1250 Unresolved non-hydrogen dihedrals: 766 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'ASN:plan1': 30, 'ASP:plan': 36, 'GLN:plan1': 18, 'HIS:plan': 2, 'GLU:plan': 24, 'ARG:plan': 14, 'PHE:plan': 8, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 585 Chain: "C" Number of atoms: 6311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 6311 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 50, 'TRANS': 895} Chain breaks: 13 Unresolved non-hydrogen bonds: 1123 Unresolved non-hydrogen angles: 1440 Unresolved non-hydrogen dihedrals: 902 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'ASP:plan': 34, 'GLN:plan1': 15, 'ASN:plan1': 32, 'GLU:plan': 22, 'PHE:plan': 16, 'TYR:plan': 16, 'ARG:plan': 14, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 647 Chain: "H" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 593 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'HIS:plan': 4, 'ASP:plan': 6, 'TRP:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 214 Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 543 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 591 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'HIS:plan': 4, 'ASP:plan': 6, 'TRP:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 214 Chain: "E" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 533 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 136 Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 591 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'HIS:plan': 4, 'ASP:plan': 6, 'TRP:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 214 Chain: "G" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 543 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.16, per 1000 atoms: 0.26 Number of scatterers: 23926 At special positions: 0 Unit cell: (128, 151, 213, 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 110 16.00 O 4494 8.00 N 4138 7.00 C 15184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.17 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.14 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.00 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.09 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 122 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C1098 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 57 sheets defined 21.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.124A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.617A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 822 removed outlier: 3.907A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.300A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 removed outlier: 4.449A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.718A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.923A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.735A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.988A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.834A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.185A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.130A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 980 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.413A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.548A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.745A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.533A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.081A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.843A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.556A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.783A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.981A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.765A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.837A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.918A pdb=" N GLU G 84 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.960A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.928A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.928A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.485A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.251A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.976A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.222A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.338A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.548A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.548A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.346A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.720A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.863A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.879A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.811A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.688A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.660A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.903A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.984A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.303A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.193A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.435A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.284A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.516A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.473A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.666A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.456A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.456A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.411A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.889A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.701A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 10 removed outlier: 6.616A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AF7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR F 33 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.553A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 11 Processing sheet with id=AG3, first strand: chain 'G' and resid 18 through 23 1213 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7428 1.33 - 1.46: 6383 1.46 - 1.59: 10426 1.59 - 1.73: 2 1.73 - 1.86: 134 Bond restraints: 24373 Sorted by residual: bond pdb=" CG LEU C1141 " pdb=" CD2 LEU C1141 " ideal model delta sigma weight residual 1.521 1.658 -0.137 3.30e-02 9.18e+02 1.73e+01 bond pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" CG LEU C1141 " pdb=" CD1 LEU C1141 " ideal model delta sigma weight residual 1.521 1.636 -0.115 3.30e-02 9.18e+02 1.21e+01 bond pdb=" CB LEU C1141 " pdb=" CG LEU C1141 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" C4 NAG C1306 " pdb=" O4 NAG C1306 " ideal model delta sigma weight residual 1.409 1.469 -0.060 2.00e-02 2.50e+03 9.03e+00 ... (remaining 24368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 33390 6.73 - 13.45: 95 13.45 - 20.18: 1 20.18 - 26.90: 1 26.90 - 33.63: 2 Bond angle restraints: 33489 Sorted by residual: angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 158.19 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C2 NAG B1312 " pdb=" N2 NAG B1312 " pdb=" C7 NAG B1312 " ideal model delta sigma weight residual 124.56 157.73 -33.17 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CD1 LEU C1141 " pdb=" CG LEU C1141 " pdb=" CD2 LEU C1141 " ideal model delta sigma weight residual 110.80 131.99 -21.19 2.20e+00 2.07e-01 9.28e+01 angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.30e-01 1.88e+00 8.78e+01 angle pdb=" N THR C 333 " pdb=" CA THR C 333 " pdb=" C THR C 333 " ideal model delta sigma weight residual 110.80 91.16 19.64 2.13e+00 2.20e-01 8.50e+01 ... (remaining 33484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14514 17.94 - 35.88: 359 35.88 - 53.83: 70 53.83 - 71.77: 31 71.77 - 89.71: 16 Dihedral angle restraints: 14990 sinusoidal: 4779 harmonic: 10211 Sorted by residual: dihedral pdb=" N THR C 333 " pdb=" C THR C 333 " pdb=" CA THR C 333 " pdb=" CB THR C 333 " ideal model delta harmonic sigma weight residual 123.40 99.74 23.66 0 2.50e+00 1.60e-01 8.96e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 177.20 -84.20 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -159.35 73.35 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 14987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3889 0.132 - 0.265: 251 0.265 - 0.397: 53 0.397 - 0.530: 0 0.530 - 0.662: 1 Chirality restraints: 4194 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.71e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.78e+01 ... (remaining 4191 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.305 2.00e-02 2.50e+03 2.58e-01 8.31e+02 pdb=" C7 NAG O 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.252 2.00e-02 2.50e+03 2.14e-01 5.75e+02 pdb=" C7 NAG C1309 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1313 " -0.148 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" C7 NAG B1313 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B1313 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG B1313 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG B1313 " -0.118 2.00e-02 2.50e+03 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8832 2.88 - 3.39: 20105 3.39 - 3.89: 37386 3.89 - 4.40: 40891 4.40 - 4.90: 70348 Nonbonded interactions: 177562 Sorted by model distance: nonbonded pdb=" O ILE B 231 " pdb=" N ILE B 233 " model vdw 2.376 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.462 3.120 nonbonded pdb=" O HIS B1083 " pdb=" OD1 ASP B1084 " model vdw 2.476 3.040 nonbonded pdb=" N ASP C 796 " pdb=" OD1 ASP C 796 " model vdw 2.487 3.120 nonbonded pdb=" O GLU B 780 " pdb=" NE2 GLN B 784 " model vdw 2.501 3.120 ... (remaining 177557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 28 or (resid 29 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 39 or (resid 40 through \ 41 and (name N or name CA or name C or name O or name CB )) or resid 42 through \ 50 or (resid 51 through 54 and (name N or name CA or name C or name O or name C \ B )) or resid 55 through 61 or (resid 62 and (name N or name CA or name C or nam \ e O or name CB )) or resid 63 through 65 or resid 82 or (resid 83 and (name N or \ name CA or name C or name O or name CB )) or resid 84 through 96 or resid 99 th \ rough 113 or (resid 116 through 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 126 or (resid 127 and (name N or name CA or na \ me C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 133 or resid 1 \ 35 through 140 or (resid 165 and (name N or name CA or name C or name O or name \ CB )) or resid 166 through 167 or (resid 168 through 171 and (name N or name CA \ or name C or name O or name CB )) or (resid 188 through 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 194 or (resid 195 thro \ ugh 198 and (name N or name CA or name C or name O or name CB )) or resid 199 th \ rough 205 or (resid 206 through 216 and (name N or name CA or name C or name O o \ r name CB )) or resid 217 through 220 or (resid 221 through 222 and (name N or n \ ame CA or name C or name O or name CB )) or resid 223 or (resid 224 and (name N \ or name CA or name C or name O or name CB )) or resid 225 through 226 or (resid \ 227 through 229 and (name N or name CA or name C or name O or name CB )) or resi \ d 230 through 234 or (resid 235 through 237 and (name N or name CA or name C or \ name O or name CB )) or resid 238 through 263 or resid 265 through 268 or (resid \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 throu \ gh 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or \ resid 282 through 286 or (resid 287 through 288 and (name N or name CA or name \ C or name O or name CB )) or resid 289 through 297 or (resid 298 and (name N or \ name CA or name C or name O or name CB )) or resid 299 through 304 or (resid 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 or (resid \ 307 and (name N or name CA or name C or name O or name CB )) or resid 308 throu \ gh 315 or (resid 316 through 317 and (name N or name CA or name C or name O or n \ ame CB )) or resid 318 or (resid 319 and (name N or name CA or name C or name O \ or name CB )) or resid 320 or (resid 321 and (name N or name CA or name C or nam \ e O or name CB )) or resid 322 or (resid 323 through 327 and (name N or name CA \ or name C or name O or name CB )) or resid 328 through 331 or (resid 332 through \ 335 and (name N or name CA or name C or name O or name CB )) or resid 336 throu \ gh 337 or (resid 338 and (name N or name CA or name C or name O or name CB )) or \ (resid 339 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 or (resid 362 through 370 and (name N or name CA or name C or name \ O or name CB )) or (resid 374 through 378 and (name N or name CA or name C or n \ ame O or name CB )) or resid 379 or (resid 380 and (name N or name CA or name C \ or name O or name CB )) or resid 383 through 384 or (resid 385 through 390 and ( \ name N or name CA or name C or name O or name CB )) or resid 391 or (resid 392 t \ hrough 403 and (name N or name CA or name C or name O or name CB )) or (resid 40 \ 4 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 417 or (resid 418 through 425 and (name N or name CA or name C or na \ me O or name CB )) or resid 426 through 428 or (resid 429 through 430 and (name \ N or name CA or name C or name O or name CB )) or resid 431 through 432 or (resi \ d 433 through 445 and (name N or name CA or name C or name O or name CB )) or (r \ esid 446 through 462 and (name N or name CA or name C or name O or name CB )) or \ resid 463 or (resid 464 through 469 and (name N or name CA or name C or name O \ or name CB )) or (resid 492 through 495 and (name N or name CA or name C or name \ O or name CB )) or resid 496 or (resid 497 through 498 and (name N or name CA o \ r name C or name O or name CB )) or resid 499 through 500 or (resid 501 and (nam \ e N or name CA or name C or name O or name CB )) or resid 502 or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 a \ nd (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 5 \ 08 through 520 and (name N or name CA or name C or name O or name CB )) or resid \ 521 through 523 or (resid 524 and (name N or name CA or name C or name O or nam \ e CB )) or resid 525 through 530 or (resid 531 through 534 and (name N or name C \ A or name C or name O or name CB )) or resid 535 or (resid 536 through 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 or (resid 539 t \ hrough 540 and (name N or name CA or name C or name O or name CB )) or resid 541 \ through 543 or (resid 544 and (name N or name CA or name C or name O or name CB \ )) or resid 545 through 546 or (resid 547 and (name N or name CA or name C or n \ ame O or name CB )) or resid 548 or (resid 549 and (name N or name CA or name C \ or name O or name CB )) or resid 550 or (resid 551 and (name N or name CA or nam \ e C or name O or name CB )) or resid 552 or (resid 553 through 556 and (name N o \ r name CA or name C or name O or name CB )) or resid 557 through 563 or (resid 5 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 565 through \ 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) or r \ esid 579 or (resid 580 through 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 through 587 or (resid 588 and (name N or name CA or nam \ e C or name O or name CB )) or resid 589 through 598 or (resid 599 and (name N o \ r name CA or name C or name O or name CB )) or resid 600 through 605 or (resid 6 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 607 through \ 617 or (resid 618 through 619 and (name N or name CA or name C or name O or nam \ e CB )) or resid 620 or (resid 641 and (name N or name CA or name C or name O or \ name CB )) or resid 642 through 644 or (resid 645 through 647 and (name N or na \ me CA or name C or name O or name CB )) or resid 648 through 662 or (resid 663 a \ nd (name N or name CA or name C or name O or name CB )) or resid 664 through 695 \ or (resid 696 and (name N or name CA or name C or name O or name CB )) or resid \ 697 through 703 or (resid 704 and (name N or name CA or name C or name O or nam \ e CB )) or resid 705 through 722 or (resid 723 through 724 and (name N or name C \ A or name C or name O or name CB )) or resid 725 through 729 or (resid 730 and ( \ name N or name CA or name C or name O or name CB )) or resid 731 or (resid 732 a \ nd (name N or name CA or name C or name O or name CB )) or resid 733 through 735 \ or (resid 736 through 737 and (name N or name CA or name C or name O or name CB \ )) or resid 738 through 745 or (resid 746 through 748 and (name N or name CA or \ name C or name O or name CB )) or resid 749 or (resid 750 and (name N or name C \ A or name C or name O or name CB )) or resid 751 through 757 or (resid 758 and ( \ name N or name CA or name C or name O or name CB )) or resid 759 through 760 or \ (resid 761 through 762 and (name N or name CA or name C or name O or name CB )) \ or resid 763 through 779 or (resid 780 and (name N or name CA or name C or name \ O or name CB )) or resid 781 through 790 or (resid 791 and (name N or name CA or \ name C or name O or name CB )) or resid 792 through 793 or (resid 794 through 7 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 797 through \ 803 or (resid 804 and (name N or name CA or name C or name O or name CB )) or r \ esid 805 through 807 or (resid 808 and (name N or name CA or name C or name O or \ name CB )) or resid 809 through 812 or (resid 813 through 814 and (name N or na \ me CA or name C or name O or name CB )) or resid 815 or (resid 816 and (name N o \ r name CA or name C or name O or name CB )) or resid 817 through 819 or (resid 8 \ 20 through 821 and (name N or name CA or name C or name O or name CB )) or resid \ 822 through 826 or (resid 856 and (name N or name CA or name C or name O or nam \ e CB )) or resid 857 through 858 or (resid 859 and (name N or name CA or name C \ or name O or name CB )) or resid 860 through 865 or (resid 866 through 868 and ( \ name N or name CA or name C or name O or name CB )) or resid 869 through 874 or \ (resid 875 through 876 and (name N or name CA or name C or name O or name CB )) \ or resid 877 through 886 or (resid 887 and (name N or name CA or name C or name \ O or name CB )) or resid 888 through 917 or (resid 918 and (name N or name CA or \ name C or name O or name CB )) or resid 919 through 948 or (resid 949 through 9 \ 50 and (name N or name CA or name C or name O or name CB )) or resid 951 through \ 963 or (resid 964 and (name N or name CA or name C or name O or name CB )) or r \ esid 965 through 972 or (resid 973 through 975 and (name N or name CA or name C \ or name O or name CB )) or resid 976 through 980 or (resid 981 through 985 and ( \ name N or name CA or name C or name O or name CB )) or resid 986 through 1002 or \ (resid 1003 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 004 through 1016 or (resid 1017 and (name N or name CA or name C or name O or na \ me CB )) or resid 1018 through 1020 or (resid 1021 through 1022 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1023 through 1036 or (resid 10 \ 37 through 1038 and (name N or name CA or name C or name O or name CB )) or resi \ d 1039 through 1072 or (resid 1073 and (name N or name CA or name C or name O or \ name CB )) or resid 1074 through 1104 or (resid 1105 and (name N or name CA or \ name C or name O or name CB )) or resid 1106 through 1110 or (resid 1111 and (na \ me N or name CA or name C or name O or name CB )) or resid 1112 through 1116 or \ (resid 1117 through 1118 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1119 through 1127 or (resid 1128 and (name N or name CA or name C or \ name O or name CB )) or resid 1129 through 1132 or (resid 1133 and (name N or na \ me CA or name C or name O or name CB )) or resid 1134 through 1312)) selection = (chain 'B' and (resid 27 through 44 or (resid 45 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 49 or (resid 50 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 65 or resid 82 through 104 or (resid 105 and (name N or name CA or name C or na \ me O or name CB )) or resid 106 through 113 or (resid 116 through 118 and (name \ N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 throug \ h 122 and (name N or name CA or name C or name O or name CB )) or (resid 126 thr \ ough 127 and (name N or name CA or name C or name O or name CB )) or resid 128 t \ hrough 140 or (resid 165 and (name N or name CA or name C or name O or name CB ) \ ) or resid 166 through 171 or (resid 188 through 191 and (name N or name CA or n \ ame C or name O or name CB )) or resid 192 through 202 or (resid 203 and (name N \ or name CA or name C or name O or name CB )) or resid 204 or (resid 205 through \ 210 and (name N or name CA or name C or name O or name CB )) or resid 215 throu \ gh 220 or (resid 221 through 222 and (name N or name CA or name C or name O or n \ ame CB )) or resid 223 through 238 or (resid 239 through 264 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 297 or (resid 298 and \ (name N or name CA or name C or name O or name CB )) or resid 299 through 306 o \ r (resid 307 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 08 through 337 or (resid 338 and (name N or name CA or name C or name O or name \ CB )) or (resid 339 through 360 and (name N or name CA or name C or name O or na \ me CB )) or resid 361 through 370 or (resid 374 through 378 and (name N or name \ CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 383 through 391 or (resid 392 \ through 403 and (name N or name CA or name C or name O or name CB )) or (resid 4 \ 04 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 417 or (resid 418 through 425 and (name N or name CA or name C or n \ ame O or name CB )) or resid 426 through 428 or (resid 429 through 430 and (name \ N or name CA or name C or name O or name CB )) or resid 431 through 432 or (res \ id 433 through 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 463 or (resid 464 through 469 and (name N or name CA or name C \ or name O or name CB )) or resid 492 through 507 or (resid 508 through 517 and ( \ name N or name CA or name C or name O or name CB )) or resid 520 through 539 or \ (resid 540 and (name N or name CA or name C or name O or name CB )) or resid 541 \ through 543 or (resid 544 and (name N or name CA or name C or name O or name CB \ )) or resid 545 through 559 or (resid 560 and (name N or name CA or name C or n \ ame O or name CB )) or resid 561 through 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 through 595 or (resid 596 and ( \ name N or name CA or name C or name O or name CB )) or resid 597 through 620 or \ resid 641 through 675 or resid 690 through 695 or (resid 696 and (name N or name \ CA or name C or name O or name CB )) or resid 697 or (resid 698 and (name N or \ name CA or name C or name O or name CB )) or resid 699 through 703 or (resid 704 \ and (name N or name CA or name C or name O or name CB )) or resid 705 through 7 \ 07 or (resid 708 and (name N or name CA or name C or name O or name CB )) or res \ id 709 through 710 or (resid 711 and (name N or name CA or name C or name O or n \ ame CB )) or resid 712 through 722 or (resid 723 through 724 and (name N or name \ CA or name C or name O or name CB )) or resid 725 through 729 or (resid 730 and \ (name N or name CA or name C or name O or name CB )) or resid 731 or (resid 732 \ and (name N or name CA or name C or name O or name CB )) or resid 733 or (resid \ 734 through 737 and (name N or name CA or name C or name O or name CB )) or res \ id 738 or (resid 739 and (name N or name CA or name C or name O or name CB )) or \ resid 740 through 760 or (resid 761 through 762 and (name N or name CA or name \ C or name O or name CB )) or resid 763 through 764 or (resid 765 through 766 and \ (name N or name CA or name C or name O or name CB )) or resid 767 through 778 o \ r (resid 779 through 780 and (name N or name CA or name C or name O or name CB ) \ ) or resid 781 through 790 or (resid 791 and (name N or name CA or name C or nam \ e O or name CB )) or resid 792 through 794 or (resid 795 through 796 and (name N \ or name CA or name C or name O or name CB )) or resid 797 through 803 or (resid \ 804 and (name N or name CA or name C or name O or name CB )) or resid 805 throu \ gh 820 or (resid 821 and (name N or name CA or name C or name O or name CB )) or \ resid 822 through 824 or (resid 825 through 826 and (name N or name CA or name \ C or name O or name CB )) or (resid 856 and (name N or name CA or name C or name \ O or name CB )) or resid 857 through 865 or (resid 866 through 868 and (name N \ or name CA or name C or name O or name CB )) or resid 869 through 886 or (resid \ 887 and (name N or name CA or name C or name O or name CB )) or resid 888 throug \ h 917 or (resid 918 and (name N or name CA or name C or name O or name CB )) or \ resid 919 through 934 or (resid 935 through 941 and (name N or name CA or name C \ or name O or name CB )) or resid 942 through 946 or (resid 947 and (name N or n \ ame CA or name C or name O or name CB )) or resid 948 through 972 or (resid 973 \ through 975 and (name N or name CA or name C or name O or name CB )) or resid 97 \ 6 through 977 or (resid 978 through 979 and (name N or name CA or name C or name \ O or name CB )) or resid 980 or (resid 981 through 985 and (name N or name CA o \ r name C or name O or name CB )) or resid 986 through 987 or (resid 988 through \ 991 and (name N or name CA or name C or name O or name CB )) or resid 992 throug \ h 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1020 or (resid 1021 through 1022 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1023 through 1037 or (resid 1038 and (name \ N or name CA or name C or name O or name CB )) or resid 1039 through 1044 or (re \ sid 1045 and (name N or name CA or name C or name O or name CB )) or resid 1046 \ through 1072 or (resid 1073 and (name N or name CA or name C or name O or name C \ B )) or resid 1074 through 1083 or (resid 1084 and (name N or name CA or name C \ or name O or name CB )) or resid 1085 through 1110 or (resid 1111 and (name N or \ name CA or name C or name O or name CB )) or resid 1112 through 1137 or (resid \ 1138 through 1139 and (name N or name CA or name C or name O or name CB )) or re \ sid 1140 through 1312)) selection = (chain 'C' and (resid 27 through 29 or (resid 30 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 50 or (resid 51 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) or res \ id 63 through 82 or (resid 83 and (name N or name CA or name C or name O or name \ CB )) or resid 84 through 96 or (resid 99 through 102 and (name N or name CA or \ name C or name O or name CB )) or resid 103 through 121 or (resid 122 and (name \ N or name CA or name C or name O or name CB )) or resid 126 through 129 or (res \ id 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thr \ ough 133 or resid 135 through 140 or resid 165 through 171 or (resid 188 through \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 194 or (resid 195 through 198 and (name N or name CA or name C or name O or n \ ame CB )) or resid 199 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 208 or (resid 209 through 210 and \ (name N or name CA or name C or name O or name CB )) or (resid 215 through 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 227 or (resid 228 through 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 through 234 or (resid 235 through 237 and \ (name N or name CA or name C or name O or name CB )) or resid 238 through 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 0 or (resid 271 and (name N or name CA or name C or name O or name CB )) or resi \ d 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) or \ resid 274 through 303 or (resid 304 through 305 and (name N or name CA or name C \ or name O or name CB )) or resid 306 through 316 or (resid 317 and (name N or n \ ame CA or name C or name O or name CB )) or resid 318 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or (resid \ 323 through 327 and (name N or name CA or name C or name O or name CB )) or resi \ d 328 through 532 or (resid 533 through 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name \ CA or name C or name O or name CB )) or resid 538 or (resid 539 through 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 through 550 or \ (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 2 through 559 or (resid 560 and (name N or name CA or name C or name O or name C \ B )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or \ name O or name CB )) or resid 565 through 566 or (resid 567 through 572 and (nam \ e N or name CA or name C or name O or name CB )) or resid 573 or (resid 574 thro \ ugh 575 and (name N or name CA or name C or name O or name CB )) or resid 576 th \ rough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 591 or (resid 592 and (name N or name CA or name C or name \ O or name CB )) or resid 593 through 595 or (resid 596 and (name N or name CA o \ r name C or name O or name CB )) or resid 597 through 618 or (resid 619 and (nam \ e N or name CA or name C or name O or name CB )) or resid 620 through 657 or (re \ sid 658 and (name N or name CA or name C or name O or name CB )) or resid 659 th \ rough 675 or resid 690 through 701 or (resid 702 and (name N or name CA or name \ C or name O or name CB )) or resid 703 through 764 or (resid 765 through 766 and \ (name N or name CA or name C or name O or name CB )) or resid 767 through 778 o \ r (resid 779 through 780 and (name N or name CA or name C or name O or name CB ) \ ) or resid 781 through 795 or (resid 796 and (name N or name CA or name C or nam \ e O or name CB )) or resid 797 through 819 or (resid 820 through 821 and (name N \ or name CA or name C or name O or name CB )) or resid 822 through 825 or (resid \ 826 through 856 and (name N or name CA or name C or name O or name CB )) or res \ id 857 through 928 or (resid 929 through 930 and (name N or name CA or name C or \ name O or name CB )) or resid 931 through 934 or (resid 935 through 941 and (na \ me N or name CA or name C or name O or name CB )) or resid 942 through 948 or (r \ esid 949 through 950 and (name N or name CA or name C or name O or name CB )) or \ resid 951 through 956 or (resid 957 through 958 and (name N or name CA or name \ C or name O or name CB )) or resid 959 through 974 or (resid 975 and (name N or \ name CA or name C or name O or name CB )) or resid 976 through 990 or (resid 991 \ and (name N or name CA or name C or name O or name CB )) or resid 992 through 1 \ 001 or (resid 1002 through 1003 and (name N or name CA or name C or name O or na \ me CB )) or resid 1004 through 1016 or (resid 1017 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1018 through 1036 or (resid 1037 through 10 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 1039 throug \ h 1104 or (resid 1105 and (name N or name CA or name C or name O or name CB )) o \ r resid 1106 through 1116 or (resid 1117 through 1118 and (name N or name CA or \ name C or name O or name CB )) or resid 1119 through 1132 or (resid 1133 and (na \ me N or name CA or name C or name O or name CB )) or resid 1134 through 1140 or \ resid 1301 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = (chain 'H' and (resid 1 through 107 or (resid 108 through 112 and (name N or nam \ e CA or name C or name O or name CB )) or resid 113 through 120)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 3 through 108) selection = (chain 'L' and resid 3 through 108) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.460 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.740 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.010 0.137 24469 Z= 0.556 Angle : 1.356 33.629 33734 Z= 0.901 Chirality : 0.077 0.662 4194 Planarity : 0.007 0.258 4404 Dihedral : 9.442 89.712 8261 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.82 % Favored : 96.78 % Rotamer: Outliers : 0.18 % Allowed : 0.83 % Favored : 99.00 % Cbeta Deviations : 0.03 % 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: 0.25 (0.13), residues: 3474 helix: -0.26 (0.18), residues: 641 sheet: 1.18 (0.16), residues: 895 loop : -0.10 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.033 0.004 TYR A 396 PHE 0.023 0.003 PHE A 898 TRP 0.018 0.004 TRP C 64 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00947 (24373) covalent geometry : angle 1.34132 (33489) SS BOND : bond 0.04330 ( 43) SS BOND : angle 3.13814 ( 86) hydrogen bonds : bond 0.18212 ( 1164) hydrogen bonds : angle 8.63651 ( 3234) link_BETA1-4 : bond 0.05488 ( 8) link_BETA1-4 : angle 2.70347 ( 24) link_NAG-ASN : bond 0.05409 ( 45) link_NAG-ASN : angle 2.29657 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 497 PHE cc_start: 0.5543 (m-80) cc_final: 0.5130 (m-80) REVERT: A 1113 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7608 (mt0) REVERT: B 544 ASN cc_start: 0.8241 (t0) cc_final: 0.7986 (t0) REVERT: B 1072 GLU cc_start: 0.7959 (pm20) cc_final: 0.7699 (pm20) REVERT: C 53 ASP cc_start: 0.7377 (t0) cc_final: 0.6967 (t0) REVERT: C 269 TYR cc_start: 0.7865 (m-80) cc_final: 0.7552 (m-80) REVERT: C 612 TYR cc_start: 0.8301 (m-80) cc_final: 0.8085 (m-80) REVERT: C 776 LYS cc_start: 0.8262 (tttp) cc_final: 0.7938 (ttpp) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.1495 time to fit residues: 69.2387 Evaluate side-chains 149 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 580 GLN A 613 GLN A 804 GLN A 955 ASN A 992 GLN A1005 GLN B 542 ASN B 644 GLN B 804 GLN B 856 ASN B 960 ASN B 992 GLN C 954 GLN C1048 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.183554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135737 restraints weight = 29597.865| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.88 r_work: 0.3259 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24469 Z= 0.189 Angle : 0.626 12.093 33734 Z= 0.328 Chirality : 0.048 0.371 4194 Planarity : 0.004 0.049 4404 Dihedral : 5.215 58.405 4780 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.53 % Favored : 98.30 % Rotamer: Outliers : 1.42 % Allowed : 4.89 % Favored : 93.69 % 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: 0.76 (0.13), residues: 3474 helix: 1.11 (0.21), residues: 645 sheet: 1.12 (0.16), residues: 961 loop : 0.02 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.020 0.002 TYR C1067 PHE 0.027 0.002 PHE A 86 TRP 0.009 0.001 TRP B 104 HIS 0.006 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00450 (24373) covalent geometry : angle 0.60285 (33489) SS BOND : bond 0.00513 ( 43) SS BOND : angle 1.21544 ( 86) hydrogen bonds : bond 0.05723 ( 1164) hydrogen bonds : angle 6.19212 ( 3234) link_BETA1-4 : bond 0.00615 ( 8) link_BETA1-4 : angle 1.82021 ( 24) link_NAG-ASN : bond 0.00607 ( 45) link_NAG-ASN : angle 2.49640 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8596 (m-10) cc_final: 0.8284 (m-80) REVERT: A 341 VAL cc_start: 0.7008 (t) cc_final: 0.6759 (m) REVERT: A 497 PHE cc_start: 0.5592 (m-80) cc_final: 0.4541 (m-80) REVERT: A 1113 GLN cc_start: 0.8629 (mm-40) cc_final: 0.7628 (mt0) REVERT: B 298 GLU cc_start: 0.8364 (tp30) cc_final: 0.8046 (tt0) REVERT: B 544 ASN cc_start: 0.8810 (t0) cc_final: 0.8361 (t0) REVERT: B 737 ASP cc_start: 0.8409 (t0) cc_final: 0.8114 (t0) REVERT: B 1072 GLU cc_start: 0.8681 (pm20) cc_final: 0.8309 (pm20) REVERT: C 102 ARG cc_start: 0.6719 (tpp80) cc_final: 0.6063 (tpp-160) REVERT: C 231 ILE cc_start: 0.7647 (mm) cc_final: 0.7372 (mt) REVERT: C 269 TYR cc_start: 0.8705 (m-80) cc_final: 0.8130 (m-10) REVERT: C 612 TYR cc_start: 0.8843 (m-80) cc_final: 0.8547 (m-80) REVERT: C 658 ASN cc_start: 0.7683 (t0) cc_final: 0.7470 (t0) REVERT: C 772 VAL cc_start: 0.8470 (t) cc_final: 0.8125 (m) REVERT: C 776 LYS cc_start: 0.8322 (tttp) cc_final: 0.7966 (ttpp) outliers start: 24 outliers final: 15 residues processed: 179 average time/residue: 0.1454 time to fit residues: 43.6958 Evaluate side-chains 160 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 63 optimal weight: 0.6980 chunk 71 optimal weight: 0.0980 chunk 139 optimal weight: 0.6980 chunk 294 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 327 optimal weight: 40.0000 chunk 296 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 856 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.182749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120191 restraints weight = 29767.793| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.90 r_work: 0.3251 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24469 Z= 0.131 Angle : 0.544 11.915 33734 Z= 0.278 Chirality : 0.046 0.335 4194 Planarity : 0.004 0.041 4404 Dihedral : 4.707 59.942 4779 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.01 % Rotamer: Outliers : 1.53 % Allowed : 5.48 % Favored : 92.98 % 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: 0.87 (0.14), residues: 3474 helix: 1.69 (0.21), residues: 624 sheet: 1.04 (0.16), residues: 960 loop : 0.01 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 34 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.002 PHE A 565 TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00293 (24373) covalent geometry : angle 0.52169 (33489) SS BOND : bond 0.00279 ( 43) SS BOND : angle 0.82306 ( 86) hydrogen bonds : bond 0.04459 ( 1164) hydrogen bonds : angle 5.42820 ( 3234) link_BETA1-4 : bond 0.00588 ( 8) link_BETA1-4 : angle 1.29022 ( 24) link_NAG-ASN : bond 0.00540 ( 45) link_NAG-ASN : angle 2.39010 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.6848 (m-80) cc_final: 0.6445 (m-80) REVERT: A 657 ASN cc_start: 0.7491 (m-40) cc_final: 0.7259 (m-40) REVERT: A 773 GLU cc_start: 0.7768 (tt0) cc_final: 0.7430 (tt0) REVERT: A 1005 GLN cc_start: 0.8823 (tt0) cc_final: 0.8620 (mt0) REVERT: B 298 GLU cc_start: 0.8360 (tp30) cc_final: 0.8061 (tt0) REVERT: B 544 ASN cc_start: 0.8727 (t0) cc_final: 0.8353 (t0) REVERT: B 589 PRO cc_start: 0.7956 (Cg_exo) cc_final: 0.7734 (Cg_endo) REVERT: B 754 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7850 (mp) REVERT: B 1072 GLU cc_start: 0.8804 (pm20) cc_final: 0.8545 (pm20) REVERT: C 102 ARG cc_start: 0.6732 (tpp80) cc_final: 0.5786 (tpm170) REVERT: C 231 ILE cc_start: 0.7491 (mm) cc_final: 0.7168 (mt) REVERT: C 269 TYR cc_start: 0.8714 (m-80) cc_final: 0.8123 (m-10) REVERT: C 658 ASN cc_start: 0.7618 (t0) cc_final: 0.7394 (t0) REVERT: C 697 MET cc_start: 0.8290 (ptm) cc_final: 0.8064 (ptp) REVERT: C 772 VAL cc_start: 0.8526 (t) cc_final: 0.8131 (m) REVERT: C 776 LYS cc_start: 0.8404 (tttp) cc_final: 0.8037 (ttpp) REVERT: C 1050 MET cc_start: 0.8857 (ptm) cc_final: 0.8616 (ptm) outliers start: 26 outliers final: 16 residues processed: 179 average time/residue: 0.1383 time to fit residues: 42.2218 Evaluate side-chains 159 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 287 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 219 optimal weight: 50.0000 chunk 255 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 655 HIS B 804 GLN B 856 ASN C 954 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132515 restraints weight = 29915.591| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.39 r_work: 0.3184 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24469 Z= 0.191 Angle : 0.589 16.066 33734 Z= 0.295 Chirality : 0.048 0.491 4194 Planarity : 0.004 0.041 4404 Dihedral : 4.852 58.177 4779 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.90 % Favored : 97.90 % Rotamer: Outliers : 2.12 % Allowed : 6.25 % Favored : 91.63 % 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: 0.71 (0.14), residues: 3474 helix: 1.48 (0.21), residues: 642 sheet: 1.00 (0.16), residues: 931 loop : -0.10 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.021 0.002 TYR A1067 PHE 0.019 0.002 PHE A 906 TRP 0.011 0.001 TRP C 886 HIS 0.007 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00461 (24373) covalent geometry : angle 0.56382 (33489) SS BOND : bond 0.00422 ( 43) SS BOND : angle 0.92370 ( 86) hydrogen bonds : bond 0.04762 ( 1164) hydrogen bonds : angle 5.32723 ( 3234) link_BETA1-4 : bond 0.00447 ( 8) link_BETA1-4 : angle 1.27910 ( 24) link_NAG-ASN : bond 0.00617 ( 45) link_NAG-ASN : angle 2.64365 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.6898 (m-80) cc_final: 0.6440 (m-80) REVERT: A 751 ASN cc_start: 0.8876 (m-40) cc_final: 0.8635 (m-40) REVERT: A 1005 GLN cc_start: 0.8814 (tt0) cc_final: 0.8610 (mt0) REVERT: B 298 GLU cc_start: 0.8342 (tp30) cc_final: 0.8036 (tt0) REVERT: B 589 PRO cc_start: 0.7986 (Cg_exo) cc_final: 0.7768 (Cg_endo) REVERT: B 754 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 1072 GLU cc_start: 0.8921 (pm20) cc_final: 0.8662 (pm20) REVERT: C 102 ARG cc_start: 0.6668 (tpp80) cc_final: 0.5888 (tpm170) REVERT: C 231 ILE cc_start: 0.7470 (mm) cc_final: 0.7145 (mt) REVERT: C 269 TYR cc_start: 0.8761 (m-80) cc_final: 0.8253 (m-80) REVERT: C 658 ASN cc_start: 0.7707 (t0) cc_final: 0.7479 (t0) REVERT: C 772 VAL cc_start: 0.8477 (t) cc_final: 0.8088 (m) REVERT: C 776 LYS cc_start: 0.8247 (tttp) cc_final: 0.7910 (ttpp) REVERT: C 1050 MET cc_start: 0.8837 (ptm) cc_final: 0.8626 (ptm) outliers start: 36 outliers final: 23 residues processed: 178 average time/residue: 0.1363 time to fit residues: 41.4908 Evaluate side-chains 159 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 45 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 280 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132344 restraints weight = 29728.792| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.88 r_work: 0.3205 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24469 Z= 0.175 Angle : 0.555 9.986 33734 Z= 0.280 Chirality : 0.047 0.296 4194 Planarity : 0.004 0.040 4404 Dihedral : 4.814 57.730 4779 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.99 % Rotamer: Outliers : 2.06 % Allowed : 7.13 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3474 helix: 1.57 (0.21), residues: 633 sheet: 0.93 (0.16), residues: 934 loop : -0.11 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE A 565 TRP 0.010 0.001 TRP C 886 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00422 (24373) covalent geometry : angle 0.53501 (33489) SS BOND : bond 0.00408 ( 43) SS BOND : angle 0.99802 ( 86) hydrogen bonds : bond 0.04583 ( 1164) hydrogen bonds : angle 5.22785 ( 3234) link_BETA1-4 : bond 0.00450 ( 8) link_BETA1-4 : angle 1.16592 ( 24) link_NAG-ASN : bond 0.00429 ( 45) link_NAG-ASN : angle 2.22586 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.6879 (m-80) cc_final: 0.6332 (m-80) REVERT: A 1005 GLN cc_start: 0.8778 (tt0) cc_final: 0.8565 (mt0) REVERT: B 298 GLU cc_start: 0.8316 (tp30) cc_final: 0.8012 (tt0) REVERT: B 754 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 102 ARG cc_start: 0.6671 (tpp80) cc_final: 0.6023 (tpm170) REVERT: C 231 ILE cc_start: 0.7510 (mm) cc_final: 0.7163 (mt) REVERT: C 772 VAL cc_start: 0.8451 (t) cc_final: 0.8051 (m) REVERT: C 776 LYS cc_start: 0.8218 (tttp) cc_final: 0.7851 (ttpp) REVERT: C 1050 MET cc_start: 0.8785 (ptm) cc_final: 0.8568 (ptm) outliers start: 35 outliers final: 26 residues processed: 162 average time/residue: 0.1443 time to fit residues: 39.5190 Evaluate side-chains 159 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 158 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 336 optimal weight: 30.0000 chunk 240 optimal weight: 0.9980 chunk 326 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 287 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 856 ASN B 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128205 restraints weight = 29808.452| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.31 r_work: 0.3166 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24469 Z= 0.222 Angle : 0.603 9.813 33734 Z= 0.305 Chirality : 0.049 0.462 4194 Planarity : 0.004 0.043 4404 Dihedral : 5.173 59.350 4779 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 6.90 % Favored : 90.62 % 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: 3474 helix: 1.46 (0.21), residues: 640 sheet: 0.81 (0.16), residues: 923 loop : -0.31 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.021 0.002 TYR A1067 PHE 0.019 0.002 PHE A 898 TRP 0.013 0.002 TRP C 886 HIS 0.008 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00547 (24373) covalent geometry : angle 0.58536 (33489) SS BOND : bond 0.00454 ( 43) SS BOND : angle 1.14801 ( 86) hydrogen bonds : bond 0.05016 ( 1164) hydrogen bonds : angle 5.28853 ( 3234) link_BETA1-4 : bond 0.00419 ( 8) link_BETA1-4 : angle 1.16241 ( 24) link_NAG-ASN : bond 0.00419 ( 45) link_NAG-ASN : angle 2.21634 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8119 (mtt) REVERT: B 298 GLU cc_start: 0.8339 (tp30) cc_final: 0.8033 (tt0) REVERT: B 754 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7599 (mp) REVERT: C 102 ARG cc_start: 0.6767 (tpp80) cc_final: 0.6167 (tpm170) REVERT: C 231 ILE cc_start: 0.7654 (mm) cc_final: 0.7352 (mt) REVERT: C 772 VAL cc_start: 0.8515 (t) cc_final: 0.8126 (m) REVERT: C 776 LYS cc_start: 0.8255 (tttp) cc_final: 0.7897 (ttpp) REVERT: C 1050 MET cc_start: 0.8783 (ptm) cc_final: 0.8580 (ptm) REVERT: C 1107 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8697 (ptt180) outliers start: 42 outliers final: 27 residues processed: 165 average time/residue: 0.1370 time to fit residues: 38.4268 Evaluate side-chains 150 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 291 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 224 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.0040 chunk 341 optimal weight: 40.0000 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132443 restraints weight = 29699.393| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.08 r_work: 0.3212 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24469 Z= 0.106 Angle : 0.520 13.450 33734 Z= 0.258 Chirality : 0.046 0.613 4194 Planarity : 0.004 0.040 4404 Dihedral : 4.806 55.768 4779 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.41 % Favored : 98.39 % Rotamer: Outliers : 1.95 % Allowed : 7.72 % Favored : 90.33 % 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: 0.69 (0.14), residues: 3474 helix: 1.88 (0.21), residues: 639 sheet: 0.88 (0.16), residues: 910 loop : -0.21 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 34 TYR 0.021 0.001 TYR A 170 PHE 0.023 0.001 PHE A 565 TRP 0.010 0.001 TRP C 886 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00232 (24373) covalent geometry : angle 0.49038 (33489) SS BOND : bond 0.00279 ( 43) SS BOND : angle 0.81696 ( 86) hydrogen bonds : bond 0.03984 ( 1164) hydrogen bonds : angle 5.00460 ( 3234) link_BETA1-4 : bond 0.00452 ( 8) link_BETA1-4 : angle 0.99048 ( 24) link_NAG-ASN : bond 0.00511 ( 45) link_NAG-ASN : angle 2.71202 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 PRO cc_start: 0.7186 (Cg_exo) cc_final: 0.6964 (Cg_endo) REVERT: A 869 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: A 1133 VAL cc_start: 0.8937 (m) cc_final: 0.8728 (p) REVERT: B 298 GLU cc_start: 0.8293 (tp30) cc_final: 0.7960 (tt0) REVERT: B 400 PHE cc_start: 0.7615 (p90) cc_final: 0.7368 (p90) REVERT: B 430 THR cc_start: 0.7956 (m) cc_final: 0.7714 (p) REVERT: B 754 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 102 ARG cc_start: 0.6661 (tpp80) cc_final: 0.6055 (tpm170) REVERT: C 231 ILE cc_start: 0.7702 (mm) cc_final: 0.7384 (mt) REVERT: C 772 VAL cc_start: 0.8466 (t) cc_final: 0.8053 (m) REVERT: C 776 LYS cc_start: 0.8250 (tttp) cc_final: 0.7861 (ttpp) REVERT: C 1050 MET cc_start: 0.8709 (ptm) cc_final: 0.8501 (ptm) outliers start: 33 outliers final: 21 residues processed: 173 average time/residue: 0.1322 time to fit residues: 39.1547 Evaluate side-chains 160 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 266 optimal weight: 0.0370 chunk 281 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 0.2980 chunk 258 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 284 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 954 GLN C1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132280 restraints weight = 29535.668| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.93 r_work: 0.3235 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24469 Z= 0.103 Angle : 0.502 12.158 33734 Z= 0.251 Chirality : 0.046 0.502 4194 Planarity : 0.004 0.039 4404 Dihedral : 4.751 56.187 4779 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.87 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 7.90 % Favored : 90.09 % 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: 0.80 (0.14), residues: 3474 helix: 1.98 (0.21), residues: 647 sheet: 0.97 (0.17), residues: 912 loop : -0.16 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.019 0.001 TYR A 170 PHE 0.014 0.001 PHE C 541 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00228 (24373) covalent geometry : angle 0.47917 (33489) SS BOND : bond 0.00264 ( 43) SS BOND : angle 0.77887 ( 86) hydrogen bonds : bond 0.03784 ( 1164) hydrogen bonds : angle 4.87138 ( 3234) link_BETA1-4 : bond 0.00431 ( 8) link_BETA1-4 : angle 0.95509 ( 24) link_NAG-ASN : bond 0.00357 ( 45) link_NAG-ASN : angle 2.34599 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6352 (p90) REVERT: A 621 PRO cc_start: 0.7134 (Cg_exo) cc_final: 0.6910 (Cg_endo) REVERT: A 869 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: A 1133 VAL cc_start: 0.8955 (m) cc_final: 0.8746 (p) REVERT: B 298 GLU cc_start: 0.8246 (tp30) cc_final: 0.7889 (tt0) REVERT: B 400 PHE cc_start: 0.7572 (p90) cc_final: 0.7360 (p90) REVERT: B 430 THR cc_start: 0.7942 (m) cc_final: 0.7728 (p) REVERT: B 754 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7615 (mp) REVERT: C 102 ARG cc_start: 0.6634 (tpp80) cc_final: 0.6059 (tpm170) REVERT: C 231 ILE cc_start: 0.7711 (mm) cc_final: 0.7391 (mt) REVERT: C 772 VAL cc_start: 0.8505 (t) cc_final: 0.8099 (m) REVERT: C 776 LYS cc_start: 0.8284 (tttp) cc_final: 0.7670 (ttpp) REVERT: C 1029 MET cc_start: 0.9165 (tpp) cc_final: 0.8869 (ttp) REVERT: C 1050 MET cc_start: 0.8678 (ptm) cc_final: 0.8466 (ptm) outliers start: 34 outliers final: 28 residues processed: 170 average time/residue: 0.1303 time to fit residues: 37.7880 Evaluate side-chains 172 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 307 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 280 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 344 optimal weight: 40.0000 chunk 93 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 chunk 184 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 804 GLN B 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.176713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129543 restraints weight = 29694.330| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.09 r_work: 0.3166 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24469 Z= 0.207 Angle : 0.590 14.077 33734 Z= 0.295 Chirality : 0.049 0.563 4194 Planarity : 0.004 0.041 4404 Dihedral : 5.186 58.563 4779 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 2.12 % Allowed : 7.90 % Favored : 89.98 % 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: 0.59 (0.14), residues: 3474 helix: 1.67 (0.21), residues: 636 sheet: 0.85 (0.17), residues: 911 loop : -0.24 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.021 0.002 TYR A1067 PHE 0.028 0.002 PHE A 565 TRP 0.009 0.001 TRP B 886 HIS 0.007 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00504 (24373) covalent geometry : angle 0.56706 (33489) SS BOND : bond 0.00435 ( 43) SS BOND : angle 0.98204 ( 86) hydrogen bonds : bond 0.04733 ( 1164) hydrogen bonds : angle 5.09039 ( 3234) link_BETA1-4 : bond 0.00373 ( 8) link_BETA1-4 : angle 1.03269 ( 24) link_NAG-ASN : bond 0.00352 ( 45) link_NAG-ASN : angle 2.53182 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7694 (p90) cc_final: 0.7450 (p90) REVERT: A 489 TYR cc_start: 0.7195 (m-80) cc_final: 0.6687 (m-80) REVERT: A 621 PRO cc_start: 0.7218 (Cg_exo) cc_final: 0.6975 (Cg_endo) REVERT: A 869 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8198 (mtt) REVERT: B 298 GLU cc_start: 0.8289 (tp30) cc_final: 0.7942 (tt0) REVERT: B 392 PHE cc_start: 0.6475 (m-80) cc_final: 0.6112 (m-80) REVERT: B 430 THR cc_start: 0.8005 (m) cc_final: 0.7766 (p) REVERT: B 754 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7627 (mp) REVERT: C 102 ARG cc_start: 0.6816 (tpp80) cc_final: 0.6178 (tpm170) REVERT: C 231 ILE cc_start: 0.7678 (mm) cc_final: 0.7357 (mt) REVERT: C 772 VAL cc_start: 0.8527 (t) cc_final: 0.8133 (m) REVERT: C 776 LYS cc_start: 0.8193 (tttp) cc_final: 0.7816 (ttpp) outliers start: 36 outliers final: 26 residues processed: 168 average time/residue: 0.1342 time to fit residues: 38.8840 Evaluate side-chains 165 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 179 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 231 optimal weight: 0.0170 chunk 124 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 0.0030 chunk 346 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132072 restraints weight = 29717.666| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.97 r_work: 0.3213 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24469 Z= 0.110 Angle : 0.511 10.912 33734 Z= 0.255 Chirality : 0.045 0.389 4194 Planarity : 0.004 0.041 4404 Dihedral : 4.843 55.925 4779 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.61 % Favored : 98.22 % Rotamer: Outliers : 1.65 % Allowed : 8.49 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3474 helix: 1.89 (0.21), residues: 651 sheet: 0.91 (0.17), residues: 905 loop : -0.15 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 34 TYR 0.025 0.001 TYR A 170 PHE 0.015 0.001 PHE C1121 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00245 (24373) covalent geometry : angle 0.48976 (33489) SS BOND : bond 0.00258 ( 43) SS BOND : angle 0.75936 ( 86) hydrogen bonds : bond 0.03916 ( 1164) hydrogen bonds : angle 4.90238 ( 3234) link_BETA1-4 : bond 0.00430 ( 8) link_BETA1-4 : angle 0.93305 ( 24) link_NAG-ASN : bond 0.00589 ( 45) link_NAG-ASN : angle 2.30967 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7640 (p90) cc_final: 0.7379 (p90) REVERT: A 489 TYR cc_start: 0.7184 (m-80) cc_final: 0.6691 (m-80) REVERT: A 621 PRO cc_start: 0.7189 (Cg_exo) cc_final: 0.6955 (Cg_endo) REVERT: A 869 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8139 (mtt) REVERT: B 298 GLU cc_start: 0.8261 (tp30) cc_final: 0.7902 (tt0) REVERT: B 392 PHE cc_start: 0.6508 (m-80) cc_final: 0.6142 (m-80) REVERT: B 754 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7627 (mp) REVERT: C 102 ARG cc_start: 0.6701 (tpp80) cc_final: 0.5944 (tpm170) REVERT: C 231 ILE cc_start: 0.7665 (mm) cc_final: 0.7345 (mt) REVERT: C 772 VAL cc_start: 0.8526 (t) cc_final: 0.8127 (m) REVERT: C 776 LYS cc_start: 0.8204 (tttp) cc_final: 0.7841 (ttpp) REVERT: C 1029 MET cc_start: 0.9194 (tpp) cc_final: 0.8897 (ttp) outliers start: 28 outliers final: 24 residues processed: 171 average time/residue: 0.1456 time to fit residues: 41.8396 Evaluate side-chains 169 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 258 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 327 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 228 optimal weight: 0.0970 chunk 301 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 856 ASN C 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.178750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131323 restraints weight = 29474.629| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.17 r_work: 0.3199 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24469 Z= 0.132 Angle : 0.521 10.610 33734 Z= 0.259 Chirality : 0.046 0.431 4194 Planarity : 0.004 0.040 4404 Dihedral : 4.778 56.526 4779 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 1.71 % Allowed : 8.73 % Favored : 89.56 % 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: 0.77 (0.14), residues: 3474 helix: 1.87 (0.21), residues: 653 sheet: 0.92 (0.17), residues: 910 loop : -0.13 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.020 0.001 TYR A 170 PHE 0.025 0.001 PHE A 565 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00313 (24373) covalent geometry : angle 0.49729 (33489) SS BOND : bond 0.00300 ( 43) SS BOND : angle 0.79775 ( 86) hydrogen bonds : bond 0.04013 ( 1164) hydrogen bonds : angle 4.88078 ( 3234) link_BETA1-4 : bond 0.00406 ( 8) link_BETA1-4 : angle 0.92175 ( 24) link_NAG-ASN : bond 0.00338 ( 45) link_NAG-ASN : angle 2.43821 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7526.93 seconds wall clock time: 128 minutes 33.29 seconds (7713.29 seconds total)