Starting phenix.real_space_refine on Fri Mar 6 06:29:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sg4_25105/03_2026/7sg4_25105.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.149 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 149 5.16 5 C 18210 2.51 5 N 4743 2.21 5 O 5607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 28709 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "B" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "C" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "H" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1239 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 6, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG:plan': 6, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 291 Chain: "L" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1237 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 9, 'GLN:plan1': 11, 'TYR:plan': 8, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 299 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 5.87, per 1000 atoms: 0.20 Number of scatterers: 28709 At special positions: 0 Unit cell: (150.12, 143.64, 218.16, 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 149 16.00 O 5607 8.00 N 4743 7.00 C 18210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.01 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.04 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A1116 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 783 " " NAG A1307 " - " ASN A 699 " " NAG A1308 " - " ASN A 691 " " NAG A1309 " - " ASN A 602 " " NAG A1310 " - " ASN A 589 " " NAG A1311 " - " ASN A 357 " " NAG A1312 " - " ASN A 330 " " NAG A1313 " - " ASN A 318 " " NAG A1314 " - " ASN A 269 " " NAG A1315 " - " ASN A 227 " " NAG A1316 " - " ASN A 158 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B1116 " " NAG B1304 " - " ASN B1080 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 783 " " NAG B1307 " - " ASN B 699 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 589 " " NAG B1311 " - " ASN B 357 " " NAG B1312 " - " ASN B 330 " " NAG B1313 " - " ASN B 318 " " NAG B1314 " - " ASN B 269 " " NAG B1315 " - " ASN B 227 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C1116 " " NAG C1304 " - " ASN C1080 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 783 " " NAG C1307 " - " ASN C 699 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 602 " " NAG C1310 " - " ASN C 589 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 330 " " NAG C1313 " - " ASN C 318 " " NAG C1314 " - " ASN C 269 " " NAG C1315 " - " ASN C 227 " " NAG C1316 " - " ASN C 158 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6986 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 54 sheets defined 24.1% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 324 through 330 removed outlier: 4.366A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.534A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 664 through 670 removed outlier: 3.857A pdb=" N SER A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.987A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.667A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.564A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.693A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.554A pdb=" N LEU A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.467A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'B' and resid 167 through 173 removed outlier: 4.474A pdb=" N VAL B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 351 through 358 removed outlier: 4.143A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.680A pdb=" N ASN B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.246A pdb=" N TYR B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.627A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.929A pdb=" N ARG B 620 " --> pdb=" O PRO B 617 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 621' Processing helix chain 'B' and resid 664 through 672 removed outlier: 6.731A pdb=" N THR B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.653A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.757A pdb=" N ASN B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.622A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.629A pdb=" N GLY B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.861A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 950 removed outlier: 3.527A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.289A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1128 Processing helix chain 'C' and resid 131 through 135 removed outlier: 4.359A pdb=" N ASP C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.503A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 removed outlier: 4.301A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.644A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 602 through 607 removed outlier: 3.690A pdb=" N SER C 607 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 719 through 726 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.507A pdb=" N GLN C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.670A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.659A pdb=" N GLY C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.685A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.800A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.522A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.160A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1128 Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.751A pdb=" N THR H 28 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'L' and resid 48 through 52 removed outlier: 4.443A pdb=" N SER L 52 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 123 through 131 removed outlier: 6.593A pdb=" N GLY L 128 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR L 129 " --> pdb=" O LYS L 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA L 130 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 182 through 184 No H-bonds generated for 'chain 'L' and resid 182 through 184' Processing helix chain 'L' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.015A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 252 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.686A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.388A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 6.294A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.814A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 363 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.714A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 439 removed outlier: 7.862A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.133A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.630A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.630A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.625A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.030A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.895A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.389A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 6.548A pdb=" N GLY B 311 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ASN B 528 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.816A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 363 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC6, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.029A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.815A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.381A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.381A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1105 removed outlier: 3.821A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.019A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.502A pdb=" N PHE C 59 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.681A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.345A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 314 removed outlier: 6.676A pdb=" N GLY C 311 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN C 528 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.906A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.029A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.150A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 693 through 710 removed outlier: 7.032A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 7.032A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.478A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE7, first strand: chain 'C' and resid 1102 through 1105 removed outlier: 3.609A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.050A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.113A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 121 through 122 Processing sheet with id=AF3, first strand: chain 'H' and resid 137 through 139 Processing sheet with id=AF4, first strand: chain 'H' and resid 154 through 155 removed outlier: 3.518A pdb=" N TRP H 154 " --> pdb=" O ILE H 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 169 through 171 removed outlier: 3.905A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AF7, first strand: chain 'L' and resid 33 through 37 Processing sheet with id=AF8, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.977A pdb=" N THR L 172 " --> pdb=" O GLN L 166 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN L 166 " --> pdb=" O THR L 172 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 144 through 146 removed outlier: 3.535A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7979 1.34 - 1.46: 5312 1.46 - 1.58: 15863 1.58 - 1.70: 0 1.70 - 1.83: 203 Bond restraints: 29357 Sorted by residual: bond pdb=" CA ASN B 626 " pdb=" C ASN B 626 " ideal model delta sigma weight residual 1.520 1.566 -0.047 1.12e-02 7.97e+03 1.73e+01 bond pdb=" N GLY B 625 " pdb=" CA GLY B 625 " ideal model delta sigma weight residual 1.446 1.491 -0.045 1.11e-02 8.12e+03 1.64e+01 bond pdb=" CA PRO A 469 " pdb=" C PRO A 469 " ideal model delta sigma weight residual 1.517 1.553 -0.036 9.30e-03 1.16e+04 1.52e+01 bond pdb=" CA VAL H 109 " pdb=" CB VAL H 109 " ideal model delta sigma weight residual 1.553 1.525 0.028 7.40e-03 1.83e+04 1.43e+01 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 29352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 39040 4.37 - 8.75: 978 8.75 - 13.12: 17 13.12 - 17.50: 0 17.50 - 21.87: 4 Bond angle restraints: 40039 Sorted by residual: angle pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " pdb=" CG1 VAL C 66 " ideal model delta sigma weight residual 110.40 132.27 -21.87 1.70e+00 3.46e-01 1.66e+02 angle pdb=" N PRO A 470 " pdb=" CA PRO A 470 " pdb=" C PRO A 470 " ideal model delta sigma weight residual 112.47 133.86 -21.39 2.06e+00 2.36e-01 1.08e+02 angle pdb=" N PRO B 470 " pdb=" CA PRO B 470 " pdb=" C PRO B 470 " ideal model delta sigma weight residual 112.47 132.61 -20.14 2.06e+00 2.36e-01 9.56e+01 angle pdb=" N PRO C 470 " pdb=" CA PRO C 470 " pdb=" C PRO C 470 " ideal model delta sigma weight residual 112.47 132.25 -19.78 2.06e+00 2.36e-01 9.22e+01 angle pdb=" CA PHE B 545 " pdb=" CB PHE B 545 " pdb=" CG PHE B 545 " ideal model delta sigma weight residual 113.80 121.90 -8.10 1.00e+00 1.00e+00 6.56e+01 ... (remaining 40034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16651 17.86 - 35.72: 1171 35.72 - 53.57: 191 53.57 - 71.43: 54 71.43 - 89.29: 23 Dihedral angle restraints: 18090 sinusoidal: 7221 harmonic: 10869 Sorted by residual: dihedral pdb=" N PRO A 470 " pdb=" C PRO A 470 " pdb=" CA PRO A 470 " pdb=" CB PRO A 470 " ideal model delta harmonic sigma weight residual 115.10 151.21 -36.11 0 2.50e+00 1.60e-01 2.09e+02 dihedral pdb=" N PRO B 470 " pdb=" C PRO B 470 " pdb=" CA PRO B 470 " pdb=" CB PRO B 470 " ideal model delta harmonic sigma weight residual 115.10 151.14 -36.04 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" N PRO C 470 " pdb=" C PRO C 470 " pdb=" CA PRO C 470 " pdb=" CB PRO C 470 " ideal model delta harmonic sigma weight residual 115.10 150.94 -35.84 0 2.50e+00 1.60e-01 2.06e+02 ... (remaining 18087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.319: 4648 0.319 - 0.639: 38 0.639 - 0.958: 1 0.958 - 1.278: 0 1.278 - 1.597: 9 Chirality restraints: 4696 Sorted by residual: chirality pdb=" CA PRO A 470 " pdb=" N PRO A 470 " pdb=" C PRO A 470 " pdb=" CB PRO A 470 " both_signs ideal model delta sigma weight residual False 2.72 1.12 1.60 2.00e-01 2.50e+01 6.38e+01 chirality pdb=" CA PRO B 470 " pdb=" N PRO B 470 " pdb=" C PRO B 470 " pdb=" CB PRO B 470 " both_signs ideal model delta sigma weight residual False 2.72 1.14 1.58 2.00e-01 2.50e+01 6.25e+01 chirality pdb=" CA PRO C 470 " pdb=" N PRO C 470 " pdb=" C PRO C 470 " pdb=" CB PRO C 470 " both_signs ideal model delta sigma weight residual False 2.72 1.15 1.57 2.00e-01 2.50e+01 6.17e+01 ... (remaining 4693 not shown) Planarity restraints: 5229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 158 " -0.147 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" CG ASN A 158 " 0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN A 158 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 158 " 0.216 2.00e-02 2.50e+03 pdb=" C1 NAG A1316 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.138 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN C 109 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.219 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.191 2.00e-02 2.50e+03 1.02e-01 2.61e+02 pdb=" CG TRP A 868 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.081 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " -0.131 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.140 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.095 2.00e-02 2.50e+03 ... (remaining 5226 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 15221 3.01 - 3.48: 29130 3.48 - 3.95: 47335 3.95 - 4.43: 53028 4.43 - 4.90: 86469 Nonbonded interactions: 231183 Sorted by model distance: nonbonded pdb=" OD1 ASP A 554 " pdb=" OG SER A 556 " model vdw 2.531 3.040 nonbonded pdb=" OH TYR B 383 " pdb=" OE1 GLU B 502 " model vdw 2.542 3.040 nonbonded pdb=" OE1 GLU A 294 " pdb=" OG1 THR A 588 " model vdw 2.552 3.040 nonbonded pdb=" OE1 GLU B 294 " pdb=" OG1 THR B 588 " model vdw 2.555 3.040 nonbonded pdb=" OE1 GLU C 294 " pdb=" OG1 THR C 588 " model vdw 2.556 3.040 ... (remaining 231178 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 35 through 1315) selection = chain 'B' selection = (chain 'C' and resid 35 through 1315) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.630 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.014 0.075 29447 Z= 0.791 Angle : 1.930 21.874 40266 Z= 1.257 Chirality : 0.123 1.597 4696 Planarity : 0.015 0.167 5182 Dihedral : 13.177 89.288 10975 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 1.58 % Allowed : 9.53 % Favored : 88.89 % Rotamer: Outliers : 2.01 % Allowed : 4.85 % Favored : 93.14 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.12), residues: 3727 helix: -1.15 (0.16), residues: 725 sheet: -0.08 (0.21), residues: 517 loop : -1.92 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 495 TYR 0.219 0.025 TYR L 92 PHE 0.141 0.015 PHE C 47 TRP 0.191 0.031 TRP A 868 HIS 0.010 0.003 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.01355 (29357) covalent geometry : angle 1.91070 (40039) SS BOND : bond 0.00869 ( 43) SS BOND : angle 1.48443 ( 86) hydrogen bonds : bond 0.17558 ( 1025) hydrogen bonds : angle 8.54225 ( 2799) link_NAG-ASN : bond 0.01447 ( 47) link_NAG-ASN : angle 5.01935 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 96 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 884 MET cc_start: 0.9119 (mmm) cc_final: 0.8808 (tpt) REVERT: B 1032 MET cc_start: 0.8552 (ptp) cc_final: 0.8248 (ptp) REVERT: C 379 PHE cc_start: 0.8493 (m-80) cc_final: 0.8139 (m-80) REVERT: H 100 SER cc_start: 0.6666 (p) cc_final: 0.6392 (m) outliers start: 59 outliers final: 26 residues processed: 154 average time/residue: 0.1682 time to fit residues: 43.6569 Evaluate side-chains 104 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 149 HIS A 178 ASN A 214 ASN A 409 ASN A 479 ASN A 721 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 737 GLN B 835 GLN L 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.069712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045821 restraints weight = 172250.808| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.46 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29447 Z= 0.164 Angle : 0.801 13.713 40266 Z= 0.420 Chirality : 0.051 0.449 4696 Planarity : 0.005 0.053 5182 Dihedral : 8.630 59.964 5030 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.67 % Favored : 92.06 % Rotamer: Outliers : 1.71 % Allowed : 6.52 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.53 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 3727 helix: 0.94 (0.19), residues: 715 sheet: -0.61 (0.18), residues: 709 loop : -1.54 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.025 0.002 TYR C 622 PHE 0.029 0.002 PHE A 451 TRP 0.019 0.002 TRP C 423 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00351 (29357) covalent geometry : angle 0.76850 (40039) SS BOND : bond 0.00294 ( 43) SS BOND : angle 1.02238 ( 86) hydrogen bonds : bond 0.05129 ( 1025) hydrogen bonds : angle 6.29542 ( 2799) link_NAG-ASN : bond 0.00679 ( 47) link_NAG-ASN : angle 3.87125 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 88 time to evaluate : 0.933 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 166 ASP cc_start: 0.8623 (m-30) cc_final: 0.8069 (t70) REVERT: A 190 LYS cc_start: 0.8851 (pttt) cc_final: 0.8544 (pttp) REVERT: A 352 TYR cc_start: 0.7902 (t80) cc_final: 0.7701 (t80) REVERT: A 374 LEU cc_start: 0.7646 (mt) cc_final: 0.7377 (mp) REVERT: B 107 MET cc_start: 0.7973 (mpp) cc_final: 0.7578 (mmm) REVERT: B 151 MET cc_start: 0.2644 (mmt) cc_final: 0.2233 (mmp) REVERT: B 476 TRP cc_start: 0.6395 (OUTLIER) cc_final: 0.6172 (t60) REVERT: B 884 MET cc_start: 0.9144 (mmm) cc_final: 0.8759 (tpt) REVERT: C 379 PHE cc_start: 0.8491 (m-80) cc_final: 0.8265 (m-80) REVERT: H 100 SER cc_start: 0.7371 (p) cc_final: 0.7134 (m) REVERT: L 27 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7593 (pm20) outliers start: 50 outliers final: 32 residues processed: 131 average time/residue: 0.1652 time to fit residues: 36.2008 Evaluate side-chains 113 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 329 optimal weight: 30.0000 chunk 277 optimal weight: 9.9990 chunk 359 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 43 optimal weight: 0.0070 chunk 189 optimal weight: 5.9990 chunk 262 optimal weight: 50.0000 overall best weight: 5.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 786 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 ASN C 381 ASN H 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.068634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.044151 restraints weight = 167393.902| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 5.00 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 29447 Z= 0.264 Angle : 0.790 13.155 40266 Z= 0.411 Chirality : 0.051 0.450 4696 Planarity : 0.005 0.051 5182 Dihedral : 8.141 58.351 5016 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.93 % Favored : 90.82 % Rotamer: Outliers : 2.08 % Allowed : 7.30 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3727 helix: 1.14 (0.20), residues: 726 sheet: -0.49 (0.19), residues: 694 loop : -1.51 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 48 TYR 0.037 0.002 TYR C 622 PHE 0.034 0.002 PHE B 545 TRP 0.027 0.002 TRP C 423 HIS 0.015 0.002 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00612 (29357) covalent geometry : angle 0.76407 (40039) SS BOND : bond 0.00515 ( 43) SS BOND : angle 1.41848 ( 86) hydrogen bonds : bond 0.05056 ( 1025) hydrogen bonds : angle 6.13742 ( 2799) link_NAG-ASN : bond 0.00675 ( 47) link_NAG-ASN : angle 3.36540 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 81 time to evaluate : 0.904 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 166 ASP cc_start: 0.8695 (m-30) cc_final: 0.8110 (t0) REVERT: A 190 LYS cc_start: 0.8825 (pttt) cc_final: 0.8471 (pttp) REVERT: A 271 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 352 TYR cc_start: 0.7956 (t80) cc_final: 0.7703 (t80) REVERT: A 374 LEU cc_start: 0.7642 (mt) cc_final: 0.7139 (mt) REVERT: A 815 PHE cc_start: 0.6028 (p90) cc_final: 0.5749 (p90) REVERT: B 107 MET cc_start: 0.8395 (mpp) cc_final: 0.8066 (mmm) REVERT: B 884 MET cc_start: 0.9052 (mmm) cc_final: 0.8530 (tpt) REVERT: C 816 MET cc_start: 0.0144 (mtt) cc_final: -0.0163 (mpp) REVERT: L 27 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7837 (pm20) outliers start: 61 outliers final: 32 residues processed: 137 average time/residue: 0.1624 time to fit residues: 38.3500 Evaluate side-chains 110 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 262 optimal weight: 20.0000 chunk 371 optimal weight: 0.1980 chunk 278 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 365 optimal weight: 50.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 178 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS B 118 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.069901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046439 restraints weight = 160733.502| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.46 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29447 Z= 0.149 Angle : 0.676 10.124 40266 Z= 0.351 Chirality : 0.048 0.391 4696 Planarity : 0.004 0.054 5182 Dihedral : 7.659 59.306 5012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.92 % Favored : 91.92 % Rotamer: Outliers : 1.81 % Allowed : 8.12 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.96 (0.14), residues: 3727 helix: 1.48 (0.20), residues: 733 sheet: -0.52 (0.19), residues: 706 loop : -1.45 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 48 TYR 0.027 0.002 TYR C 622 PHE 0.021 0.001 PHE C 545 TRP 0.015 0.001 TRP A 423 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00331 (29357) covalent geometry : angle 0.65106 (40039) SS BOND : bond 0.00253 ( 43) SS BOND : angle 1.05440 ( 86) hydrogen bonds : bond 0.04209 ( 1025) hydrogen bonds : angle 5.75638 ( 2799) link_NAG-ASN : bond 0.00554 ( 47) link_NAG-ASN : angle 3.04449 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 79 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8794 (m-30) cc_final: 0.8264 (t0) REVERT: A 190 LYS cc_start: 0.8785 (pttt) cc_final: 0.8462 (pttp) REVERT: A 334 PHE cc_start: 0.3200 (OUTLIER) cc_final: 0.2270 (m-10) REVERT: A 352 TYR cc_start: 0.7960 (t80) cc_final: 0.7715 (t80) REVERT: A 374 LEU cc_start: 0.7799 (mt) cc_final: 0.7273 (mt) REVERT: B 107 MET cc_start: 0.8082 (mpp) cc_final: 0.7715 (mmm) REVERT: B 151 MET cc_start: 0.3253 (mmt) cc_final: 0.3047 (mmp) REVERT: B 373 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8714 (mmmt) REVERT: C 149 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8551 (t-90) REVERT: C 151 MET cc_start: 0.4457 (mmt) cc_final: 0.3508 (mmt) REVERT: C 816 MET cc_start: -0.0463 (mtt) cc_final: -0.0807 (mpp) REVERT: H 140 CYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6622 (t) REVERT: L 27 GLN cc_start: 0.8603 (mm-40) cc_final: 0.7980 (pm20) outliers start: 53 outliers final: 38 residues processed: 127 average time/residue: 0.1707 time to fit residues: 37.1455 Evaluate side-chains 117 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 99 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 258 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 365 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.068247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.043793 restraints weight = 167078.451| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.89 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29447 Z= 0.277 Angle : 0.740 14.324 40266 Z= 0.381 Chirality : 0.049 0.416 4696 Planarity : 0.005 0.054 5182 Dihedral : 7.759 59.680 5009 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.02 % Favored : 90.85 % Rotamer: Outliers : 2.01 % Allowed : 9.11 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3727 helix: 1.39 (0.20), residues: 734 sheet: -0.63 (0.19), residues: 705 loop : -1.50 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 48 TYR 0.035 0.002 TYR C 622 PHE 0.029 0.002 PHE B 545 TRP 0.018 0.002 TRP A 245 HIS 0.026 0.002 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00645 (29357) covalent geometry : angle 0.71685 (40039) SS BOND : bond 0.00305 ( 43) SS BOND : angle 0.98515 ( 86) hydrogen bonds : bond 0.04734 ( 1025) hydrogen bonds : angle 5.87976 ( 2799) link_NAG-ASN : bond 0.00655 ( 47) link_NAG-ASN : angle 3.14358 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 75 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5520 (m) REVERT: A 166 ASP cc_start: 0.8751 (m-30) cc_final: 0.8254 (p0) REVERT: A 190 LYS cc_start: 0.8813 (pttt) cc_final: 0.8483 (pttp) REVERT: A 334 PHE cc_start: 0.4115 (OUTLIER) cc_final: 0.2884 (m-10) REVERT: A 352 TYR cc_start: 0.7900 (t80) cc_final: 0.7632 (t80) REVERT: A 374 LEU cc_start: 0.7816 (mt) cc_final: 0.7366 (mt) REVERT: A 417 MET cc_start: 0.6871 (tpp) cc_final: 0.6604 (tpt) REVERT: B 107 MET cc_start: 0.8423 (mpp) cc_final: 0.8088 (mmm) REVERT: B 271 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7925 (p) REVERT: B 884 MET cc_start: 0.8904 (tpt) cc_final: 0.8437 (tpt) REVERT: C 816 MET cc_start: -0.0049 (mtt) cc_final: -0.0500 (mpp) REVERT: H 140 CYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6531 (t) REVERT: L 27 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8088 (pm20) outliers start: 59 outliers final: 39 residues processed: 130 average time/residue: 0.1599 time to fit residues: 35.8024 Evaluate side-chains 117 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 154 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 chunk 369 optimal weight: 50.0000 chunk 217 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS B 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.069952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045335 restraints weight = 161854.443| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.97 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29447 Z= 0.114 Angle : 0.635 11.843 40266 Z= 0.327 Chirality : 0.047 0.422 4696 Planarity : 0.004 0.058 5182 Dihedral : 7.343 59.449 5009 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % Rotamer: Outliers : 1.77 % Allowed : 9.42 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.84 (0.14), residues: 3727 helix: 1.82 (0.20), residues: 728 sheet: -0.56 (0.20), residues: 688 loop : -1.41 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.024 0.001 TYR C 622 PHE 0.019 0.001 PHE A 47 TRP 0.014 0.001 TRP A 423 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00238 (29357) covalent geometry : angle 0.61397 (40039) SS BOND : bond 0.00235 ( 43) SS BOND : angle 0.80556 ( 86) hydrogen bonds : bond 0.03900 ( 1025) hydrogen bonds : angle 5.51960 ( 2799) link_NAG-ASN : bond 0.00723 ( 47) link_NAG-ASN : angle 2.80389 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 77 time to evaluate : 1.077 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 107 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4469 (mpp) REVERT: A 166 ASP cc_start: 0.8640 (m-30) cc_final: 0.8347 (p0) REVERT: A 190 LYS cc_start: 0.8800 (pttt) cc_final: 0.8480 (pttp) REVERT: A 334 PHE cc_start: 0.3779 (OUTLIER) cc_final: 0.2735 (m-10) REVERT: A 352 TYR cc_start: 0.8112 (t80) cc_final: 0.7846 (t80) REVERT: A 374 LEU cc_start: 0.7846 (mt) cc_final: 0.7428 (mt) REVERT: A 770 MET cc_start: 0.8486 (mmm) cc_final: 0.8103 (mmm) REVERT: A 967 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8839 (t70) REVERT: B 107 MET cc_start: 0.8315 (mpp) cc_final: 0.7974 (mmm) REVERT: B 144 MET cc_start: -0.0571 (tmm) cc_final: -0.1396 (ttp) REVERT: B 884 MET cc_start: 0.8824 (tpt) cc_final: 0.8333 (tpt) REVERT: B 894 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (p) REVERT: C 37 MET cc_start: 0.8966 (mtm) cc_final: 0.8717 (mtm) REVERT: C 379 PHE cc_start: 0.8515 (m-80) cc_final: 0.7983 (t80) REVERT: H 140 CYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6383 (t) REVERT: L 27 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8190 (pm20) outliers start: 52 outliers final: 35 residues processed: 126 average time/residue: 0.1765 time to fit residues: 37.7475 Evaluate side-chains 115 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 967 ASP Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 330 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS B 112 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN L 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.067512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043306 restraints weight = 170599.026| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.88 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 29447 Z= 0.322 Angle : 0.752 9.949 40266 Z= 0.386 Chirality : 0.050 0.366 4696 Planarity : 0.005 0.057 5182 Dihedral : 7.715 59.678 5008 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.28 % Favored : 90.61 % Rotamer: Outliers : 1.95 % Allowed : 10.27 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3727 helix: 1.54 (0.20), residues: 716 sheet: -0.68 (0.19), residues: 696 loop : -1.51 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 48 TYR 0.041 0.002 TYR A 622 PHE 0.032 0.002 PHE B 545 TRP 0.016 0.002 TRP A 423 HIS 0.007 0.002 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00747 (29357) covalent geometry : angle 0.73112 (40039) SS BOND : bond 0.00338 ( 43) SS BOND : angle 0.96971 ( 86) hydrogen bonds : bond 0.04881 ( 1025) hydrogen bonds : angle 5.87047 ( 2799) link_NAG-ASN : bond 0.00765 ( 47) link_NAG-ASN : angle 2.99486 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 73 time to evaluate : 0.876 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 166 ASP cc_start: 0.8789 (m-30) cc_final: 0.8572 (p0) REVERT: A 190 LYS cc_start: 0.8805 (pttt) cc_final: 0.8475 (pttp) REVERT: A 271 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 334 PHE cc_start: 0.4311 (OUTLIER) cc_final: 0.3332 (m-10) REVERT: A 352 TYR cc_start: 0.7866 (t80) cc_final: 0.7567 (t80) REVERT: A 374 LEU cc_start: 0.8061 (mt) cc_final: 0.7739 (mt) REVERT: A 1076 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8821 (m) REVERT: B 107 MET cc_start: 0.8396 (mpp) cc_final: 0.8059 (mmm) REVERT: B 271 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8003 (p) REVERT: B 884 MET cc_start: 0.8875 (tpt) cc_final: 0.8456 (tpt) REVERT: H 140 CYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6489 (t) REVERT: L 27 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8086 (pm20) outliers start: 57 outliers final: 40 residues processed: 129 average time/residue: 0.1642 time to fit residues: 36.0549 Evaluate side-chains 117 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 72 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 166 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.069121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044705 restraints weight = 163299.643| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.96 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29447 Z= 0.143 Angle : 0.640 10.141 40266 Z= 0.331 Chirality : 0.047 0.361 4696 Planarity : 0.004 0.066 5182 Dihedral : 7.389 59.672 5008 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.10 % Favored : 91.79 % Rotamer: Outliers : 1.60 % Allowed : 10.72 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.91 (0.14), residues: 3727 helix: 1.76 (0.20), residues: 734 sheet: -0.66 (0.20), residues: 706 loop : -1.45 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1021 TYR 0.025 0.001 TYR C 622 PHE 0.021 0.001 PHE C 545 TRP 0.014 0.001 TRP A 423 HIS 0.022 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00321 (29357) covalent geometry : angle 0.61970 (40039) SS BOND : bond 0.00252 ( 43) SS BOND : angle 0.81957 ( 86) hydrogen bonds : bond 0.04057 ( 1025) hydrogen bonds : angle 5.56557 ( 2799) link_NAG-ASN : bond 0.00479 ( 47) link_NAG-ASN : angle 2.71401 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8776 (pttt) cc_final: 0.8503 (pttp) REVERT: A 334 PHE cc_start: 0.3985 (OUTLIER) cc_final: 0.2891 (m-10) REVERT: A 352 TYR cc_start: 0.8014 (t80) cc_final: 0.7721 (t80) REVERT: A 374 LEU cc_start: 0.8019 (mt) cc_final: 0.7752 (mt) REVERT: A 770 MET cc_start: 0.8549 (mmm) cc_final: 0.8183 (mmm) REVERT: A 1047 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 107 MET cc_start: 0.8413 (mpp) cc_final: 0.8104 (mmm) REVERT: B 144 MET cc_start: -0.0613 (tmm) cc_final: -0.1570 (ttp) REVERT: B 373 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8559 (mmmt) REVERT: B 884 MET cc_start: 0.8861 (tpt) cc_final: 0.8305 (tpt) REVERT: C 37 MET cc_start: 0.8966 (mtm) cc_final: 0.8758 (mtm) REVERT: C 144 MET cc_start: 0.5606 (pmm) cc_final: 0.5292 (pmm) REVERT: C 151 MET cc_start: 0.3788 (mmt) cc_final: 0.3212 (mmt) REVERT: C 379 PHE cc_start: 0.8539 (m-80) cc_final: 0.8045 (t80) REVERT: H 140 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6414 (t) REVERT: L 27 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8086 (pm20) outliers start: 47 outliers final: 32 residues processed: 119 average time/residue: 0.1693 time to fit residues: 34.5580 Evaluate side-chains 107 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 125 optimal weight: 10.0000 chunk 292 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 291 optimal weight: 0.0040 chunk 105 optimal weight: 6.9990 chunk 334 optimal weight: 30.0000 chunk 27 optimal weight: 0.5980 chunk 146 optimal weight: 40.0000 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 HIS ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 381 ASN B 883 GLN H 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.069205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045247 restraints weight = 166975.476| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.82 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29447 Z= 0.117 Angle : 0.609 11.273 40266 Z= 0.314 Chirality : 0.046 0.533 4696 Planarity : 0.004 0.064 5182 Dihedral : 7.069 59.306 5008 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.13 % Favored : 91.76 % Rotamer: Outliers : 1.50 % Allowed : 10.68 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3727 helix: 2.09 (0.20), residues: 726 sheet: -0.53 (0.19), residues: 736 loop : -1.44 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.023 0.001 TYR C 622 PHE 0.022 0.001 PHE A 329 TRP 0.022 0.001 TRP A 423 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00254 (29357) covalent geometry : angle 0.58933 (40039) SS BOND : bond 0.00241 ( 43) SS BOND : angle 0.75838 ( 86) hydrogen bonds : bond 0.03615 ( 1025) hydrogen bonds : angle 5.32030 ( 2799) link_NAG-ASN : bond 0.00508 ( 47) link_NAG-ASN : angle 2.63784 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 76 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8804 (pttt) cc_final: 0.8476 (pttp) REVERT: A 334 PHE cc_start: 0.4270 (OUTLIER) cc_final: 0.3276 (m-10) REVERT: A 352 TYR cc_start: 0.8111 (t80) cc_final: 0.7856 (t80) REVERT: A 374 LEU cc_start: 0.8067 (mt) cc_final: 0.7645 (mt) REVERT: B 107 MET cc_start: 0.8188 (mpp) cc_final: 0.7842 (mmm) REVERT: B 144 MET cc_start: -0.0837 (tmm) cc_final: -0.2222 (ttp) REVERT: B 884 MET cc_start: 0.8967 (tpt) cc_final: 0.8677 (tpt) REVERT: C 37 MET cc_start: 0.8934 (mtm) cc_final: 0.8702 (mtm) REVERT: C 144 MET cc_start: 0.5194 (pmm) cc_final: 0.4984 (pmm) REVERT: C 151 MET cc_start: 0.3472 (mmt) cc_final: 0.2938 (mmt) REVERT: C 374 LEU cc_start: 0.7105 (mt) cc_final: 0.6845 (mt) REVERT: C 894 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8394 (p) REVERT: H 140 CYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6318 (t) REVERT: L 27 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8236 (pm20) outliers start: 44 outliers final: 32 residues processed: 116 average time/residue: 0.1674 time to fit residues: 33.6037 Evaluate side-chains 110 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 97 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 331 optimal weight: 40.0000 chunk 345 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 193 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 HIS ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.069110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.045137 restraints weight = 166752.653| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.82 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 29447 Z= 0.197 Angle : 0.752 59.199 40266 Z= 0.404 Chirality : 0.049 0.844 4696 Planarity : 0.005 0.064 5182 Dihedral : 7.066 59.334 5006 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 1.30 % Allowed : 10.92 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3727 helix: 2.04 (0.20), residues: 726 sheet: -0.48 (0.19), residues: 727 loop : -1.44 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1021 TYR 0.024 0.001 TYR C 622 PHE 0.024 0.001 PHE C 501 TRP 0.019 0.001 TRP A 423 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00438 (29357) covalent geometry : angle 0.72583 (40039) SS BOND : bond 0.00253 ( 43) SS BOND : angle 0.81632 ( 86) hydrogen bonds : bond 0.03721 ( 1025) hydrogen bonds : angle 5.32621 ( 2799) link_NAG-ASN : bond 0.01732 ( 47) link_NAG-ASN : angle 3.37506 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8790 (pttt) cc_final: 0.8473 (pttp) REVERT: A 334 PHE cc_start: 0.4261 (OUTLIER) cc_final: 0.3279 (m-10) REVERT: A 352 TYR cc_start: 0.8111 (t80) cc_final: 0.7856 (t80) REVERT: A 374 LEU cc_start: 0.7965 (mt) cc_final: 0.7650 (mt) REVERT: B 107 MET cc_start: 0.8269 (mpp) cc_final: 0.7929 (mmm) REVERT: B 144 MET cc_start: -0.0834 (tmm) cc_final: -0.2684 (tpt) REVERT: B 884 MET cc_start: 0.8978 (tpt) cc_final: 0.8689 (tpt) REVERT: C 37 MET cc_start: 0.8945 (mtm) cc_final: 0.8713 (mtm) REVERT: C 144 MET cc_start: 0.5182 (pmm) cc_final: 0.4945 (pmm) REVERT: C 151 MET cc_start: 0.3474 (mmt) cc_final: 0.2940 (mmt) REVERT: C 379 PHE cc_start: 0.8327 (m-80) cc_final: 0.7831 (t80) REVERT: C 894 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8416 (p) REVERT: H 140 CYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6325 (t) REVERT: L 27 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8377 (pm20) outliers start: 38 outliers final: 34 residues processed: 113 average time/residue: 0.1673 time to fit residues: 32.6694 Evaluate side-chains 112 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.1980 chunk 330 optimal weight: 50.0000 chunk 270 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 chunk 46 optimal weight: 40.0000 chunk 351 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 HIS ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.069827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045530 restraints weight = 161221.272| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.89 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 29447 Z= 0.197 Angle : 0.752 59.199 40266 Z= 0.404 Chirality : 0.049 0.844 4696 Planarity : 0.005 0.064 5182 Dihedral : 7.066 59.334 5006 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 1.30 % Allowed : 10.92 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3727 helix: 2.04 (0.20), residues: 726 sheet: -0.48 (0.19), residues: 727 loop : -1.44 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1021 TYR 0.024 0.001 TYR C 622 PHE 0.024 0.001 PHE C 501 TRP 0.019 0.001 TRP A 423 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00438 (29357) covalent geometry : angle 0.72583 (40039) SS BOND : bond 0.00253 ( 43) SS BOND : angle 0.81632 ( 86) hydrogen bonds : bond 0.03721 ( 1025) hydrogen bonds : angle 5.32621 ( 2799) link_NAG-ASN : bond 0.01732 ( 47) link_NAG-ASN : angle 3.37506 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5634.34 seconds wall clock time: 97 minutes 46.58 seconds (5866.58 seconds total)