Starting phenix.real_space_refine on Mon Aug 25 12:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8i_39047/08_2025/8y8i_39047.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 170 5.16 5 C 17691 2.51 5 N 4539 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27728 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9153 Classifications: {'peptide': 1179} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1123} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 9236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9236 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 9255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9255 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.05, per 1000 atoms: 0.22 Number of scatterers: 27728 At special positions: 0 Unit cell: (157.44, 150.88, 209.92, 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 170 16.00 O 5328 8.00 N 4539 7.00 C 17691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 725 " " NAG A1302 " - " ASN A 188 " " NAG B1301 " - " ASN B 664 " " NAG B1302 " - " ASN B 58 " " NAG B1303 " - " ASN B 188 " " NAG C1301 " - " ASN C 664 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6730 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 67 sheets defined 24.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.843A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.576A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.002A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.516A pdb=" N VAL A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.749A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 813 through 818 removed outlier: 3.825A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.580A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 862 Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 901 through 911 removed outlier: 4.161A pdb=" N VAL A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.775A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.557A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.537A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 removed outlier: 4.134A pdb=" N GLY A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.762A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1021 removed outlier: 3.547A pdb=" N ALA A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1046 removed outlier: 3.534A pdb=" N ALA A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.560A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.846A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 3.568A pdb=" N ASP A1182 " --> pdb=" O LYS A1179 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.517A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.687A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.516A pdb=" N TYR C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 449' Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.539A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 781 through 785 Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.526A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 861 removed outlier: 3.809A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 911 Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.871A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR C 926 " --> pdb=" O TYR C 922 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 928 " --> pdb=" O ASN C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 4.237A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.646A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1021 Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.549A pdb=" N ILE C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1057 through 1063 removed outlier: 3.678A pdb=" N ILE C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 4.618A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.522A pdb=" N TRP B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.825A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.534A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.576A pdb=" N TYR B 448 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 449' Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.561A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 822 through 828 removed outlier: 3.848A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 841 through 862 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 4.324A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 909 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.255A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 951 through 964 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.570A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 991 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.692A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1021 removed outlier: 3.749A pdb=" N ALA B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1046 Processing helix chain 'B' and resid 1057 through 1065 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.884A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B1102 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.501A pdb=" N LEU A 261 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.803A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.513A pdb=" N SER A 173 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 160 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N HIS A 175 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N TYR A 158 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.624A pdb=" N GLY A 302 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 678 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA9, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.563A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.563A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.805A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.584A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 632 through 635 removed outlier: 4.153A pdb=" N TYR A 667 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 731 removed outlier: 3.717A pdb=" N PHE A 764 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 726 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR A 766 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER A 728 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 736 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.107A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 799 Processing sheet with id=AC2, first strand: chain 'A' and resid 794 through 799 removed outlier: 3.502A pdb=" N ALA A1137 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A1146 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 867 through 868 removed outlier: 7.274A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.711A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.530A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1178 Processing sheet with id=AC7, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AC9, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.786A pdb=" N ARG C 75 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.103A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 148 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS C 187 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.276A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 302 through 307 removed outlier: 3.659A pdb=" N LEU C 690 " --> pdb=" O LEU C 721 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 721 " --> pdb=" O LEU C 690 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 316 through 317 removed outlier: 3.516A pdb=" N THR C 668 " --> pdb=" O LYS C 634 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.732A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.732A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AD9, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AE1, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AE2, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AE3, first strand: chain 'C' and resid 730 through 731 removed outlier: 4.272A pdb=" N VAL C 731 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 773 through 775 Processing sheet with id=AE5, first strand: chain 'C' and resid 786 through 790 Processing sheet with id=AE6, first strand: chain 'C' and resid 794 through 797 Processing sheet with id=AE7, first strand: chain 'C' and resid 794 through 797 removed outlier: 6.212A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1202 through 1204 removed outlier: 3.967A pdb=" N VAL C1203 " --> pdb=" O ALA C1171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C1171 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C1170 " --> pdb=" O LEU C1162 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C1162 " --> pdb=" O ILE C1170 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 3.532A pdb=" N ILE C1178 " --> pdb=" O MET C1185 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 59 through 67 removed outlier: 7.757A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.525A pdb=" N ARG B 75 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 96 through 97 removed outlier: 4.012A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 150 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AF5, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.645A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'B' and resid 302 through 305 removed outlier: 3.673A pdb=" N GLY B 302 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 681 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AF8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.635A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.831A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.831A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.858A pdb=" N PHE B 354 " --> pdb=" O CYS B 603 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AG5, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AG7, first strand: chain 'B' and resid 647 through 649 removed outlier: 6.382A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 691 through 693 removed outlier: 3.603A pdb=" N VAL B 720 " --> pdb=" O PHE B 713 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 725 through 731 removed outlier: 11.536A pdb=" N TYR B 762 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N THR B 727 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE B 764 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR B 729 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 766 " --> pdb=" O TYR B 729 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 786 through 791 removed outlier: 6.714A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B1176 " --> pdb=" O THR B1187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B1187 " --> pdb=" O TYR B1176 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B1186 " --> pdb=" O GLU B1195 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY B1188 " --> pdb=" O TYR B1193 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 794 through 804 removed outlier: 3.921A pdb=" N ILE B 803 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B1141 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.270A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1162 through 1164 999 hydrogen bonds defined for protein. 2757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8862 1.34 - 1.46: 6988 1.46 - 1.58: 12358 1.58 - 1.70: 0 1.70 - 1.81: 197 Bond restraints: 28405 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 28400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 38381 1.74 - 3.48: 318 3.48 - 5.21: 11 5.21 - 6.95: 4 6.95 - 8.69: 1 Bond angle restraints: 38715 Sorted by residual: angle pdb=" N VAL C 481 " pdb=" CA VAL C 481 " pdb=" C VAL C 481 " ideal model delta sigma weight residual 112.96 109.53 3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA LEU C 57 " pdb=" CB LEU C 57 " pdb=" CG LEU C 57 " ideal model delta sigma weight residual 116.30 124.99 -8.69 3.50e+00 8.16e-02 6.16e+00 angle pdb=" N VAL C 482 " pdb=" CA VAL C 482 " pdb=" C VAL C 482 " ideal model delta sigma weight residual 112.98 109.91 3.07 1.25e+00 6.40e-01 6.04e+00 angle pdb=" N GLY C 833 " pdb=" CA GLY C 833 " pdb=" C GLY C 833 " ideal model delta sigma weight residual 111.35 114.00 -2.65 1.20e+00 6.94e-01 4.89e+00 angle pdb=" N PRO A1067 " pdb=" CA PRO A1067 " pdb=" C PRO A1067 " ideal model delta sigma weight residual 110.70 113.18 -2.48 1.22e+00 6.72e-01 4.15e+00 ... (remaining 38710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 16476 17.56 - 35.12: 441 35.12 - 52.68: 77 52.68 - 70.24: 9 70.24 - 87.80: 3 Dihedral angle restraints: 17006 sinusoidal: 6533 harmonic: 10473 Sorted by residual: dihedral pdb=" N VAL A 977 " pdb=" CA VAL A 977 " pdb=" CB VAL A 977 " pdb=" CG1 VAL A 977 " ideal model delta sinusoidal sigma weight residual 60.00 119.84 -59.84 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU C 726 " pdb=" CA LEU C 726 " pdb=" CB LEU C 726 " pdb=" CG LEU C 726 " ideal model delta sinusoidal sigma weight residual -60.00 -117.06 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N LYS C 696 " pdb=" CA LYS C 696 " pdb=" CB LYS C 696 " pdb=" CG LYS C 696 " ideal model delta sinusoidal sigma weight residual -180.00 -124.48 -55.52 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 17003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2724 0.028 - 0.056: 1065 0.056 - 0.084: 288 0.084 - 0.112: 268 0.112 - 0.140: 44 Chirality restraints: 4389 Sorted by residual: chirality pdb=" CA ILE C 321 " pdb=" N ILE C 321 " pdb=" C ILE C 321 " pdb=" CB ILE C 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE C1144 " pdb=" N ILE C1144 " pdb=" C ILE C1144 " pdb=" CB ILE C1144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 321 " pdb=" N ILE B 321 " pdb=" C ILE B 321 " pdb=" CB ILE B 321 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 4386 not shown) Planarity restraints: 4997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 901 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO C 902 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 902 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 902 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 623 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ASP B 623 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 623 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 624 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B1171 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B1172 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B1172 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1172 " -0.019 5.00e-02 4.00e+02 ... (remaining 4994 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2717 2.75 - 3.29: 27103 3.29 - 3.83: 44876 3.83 - 4.36: 51570 4.36 - 4.90: 90574 Nonbonded interactions: 216840 Sorted by model distance: nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.216 3.040 nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 792 " pdb=" OG SER A1152 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 123 " pdb=" O VAL C 139 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR C1148 " pdb=" O SER C1190 " model vdw 2.281 3.040 ... (remaining 216835 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 14 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 90 or (resid 91 and (name N or nam \ e CA or name C or name O or name CB )) or resid 92 through 344 or (resid 345 thr \ ough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 360 or (resid 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 378 or (resid 379 and (name N or name CA or name C or nam \ e O or name CB )) or resid 380 through 389 or (resid 390 and (name N or name CA \ or name C or name O or name CB )) or resid 391 through 520 or (resid 521 through \ 525 and (name N or name CA or name C or name O or name CB )) or resid 526 throu \ gh 606 or (resid 607 through 609 and (name N or name CA or name C or name O or n \ ame CB )) or resid 610 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB )) or resid 628 through 708 or (resid 709 and (name N or \ name CA or name C or name O or name CB )) or resid 710 through 779 or (resid 780 \ and (name N or name CA or name C or name O or name CB )) or resid 781 through 8 \ 36 or (resid 837 and (name N or name CA or name C or name O or name CB )) or res \ id 838 through 875 or (resid 876 and (name N or name CA or name C or name O or n \ ame CB )) or resid 877 through 929 or (resid 930 through 932 and (name N or name \ CA or name C or name O or name CB )) or resid 933 through 998 or (resid 999 and \ (name N or name CA or name C or name O or name CB )) or resid 1000 through 1065 \ or (resid 1066 and (name N or name CA or name C or name O or name CB )) or resi \ d 1067 through 1148 or (resid 1149 and (name N or name CA or name C or name O or \ name CB )) or resid 1150 through 1199 or (resid 1200 and (name N or name CA or \ name C or name O or name CB )) or resid 1201 through 1301)) selection = (chain 'B' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 232 or (resid 233 and \ (name N or name CA or name C or name O or name CB )) or resid 234 through 246 o \ r (resid 247 through 248 and (name N or name CA or name C or name O or name CB ) \ ) or resid 249 or (resid 250 through 253 and (name N or name CA or name C or nam \ e O or name CB )) or resid 254 through 308 or resid 317 through 344 or (resid 34 \ 5 through 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 360 or (resid 361 and (name N or name CA or name C or name O or name \ CB )) or resid 362 through 378 or (resid 379 and (name N or name CA or name C o \ r name O or name CB )) or resid 380 through 389 or (resid 390 and (name N or nam \ e CA or name C or name O or name CB )) or resid 391 through 606 or (resid 607 th \ rough 609 and (name N or name CA or name C or name O or name CB )) or resid 610 \ through 626 or (resid 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 629 or (resid 630 and (name N or name CA or name C or na \ me O or name CB )) or resid 631 through 705 or (resid 706 and (name N or name CA \ or name C or name O or name CB )) or resid 707 through 708 or (resid 709 and (n \ ame N or name CA or name C or name O or name CB )) or resid 710 through 779 or ( \ resid 780 and (name N or name CA or name C or name O or name CB )) or resid 781 \ through 836 or (resid 837 and (name N or name CA or name C or name O or name CB \ )) or resid 838 through 890 or (resid 891 and (name N or name CA or name C or na \ me O or name CB )) or resid 899 through 998 or (resid 999 and (name N or name CA \ or name C or name O or name CB )) or resid 1000 through 1199 or (resid 1200 and \ (name N or name CA or name C or name O or name CB )) or resid 1201 through 1301 \ )) selection = (chain 'C' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 232 or (resid 233 and (name N or name CA or name C or name O or name CB )) \ or resid 234 through 246 or (resid 247 through 248 and (name N or name CA or nam \ e C or name O or name CB )) or resid 249 or (resid 250 through 253 and (name N o \ r name CA or name C or name O or name CB )) or resid 254 through 308 or resid 31 \ 7 through 520 or (resid 521 through 525 and (name N or name CA or name C or name \ O or name CB )) or resid 526 through 615 or (resid 616 and (name N or name CA o \ r name C or name O or name CB )) or resid 617 through 619 or (resid 620 and (nam \ e N or name CA or name C or name O or name CB )) or resid 621 through 629 or (re \ sid 630 and (name N or name CA or name C or name O or name CB )) or resid 631 or \ (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 63 \ 3 or (resid 634 and (name N or name CA or name C or name O or name CB )) or resi \ d 635 through 651 or (resid 652 and (name N or name CA or name C or name O or na \ me CB )) or resid 653 or (resid 654 and (name N or name CA or name C or name O o \ r name CB )) or resid 655 through 875 or (resid 876 and (name N or name CA or na \ me C or name O or name CB )) or resid 877 through 890 or (resid 891 and (name N \ or name CA or name C or name O or name CB )) or resid 899 through 930 or (resid \ 931 through 932 and (name N or name CA or name C or name O or name CB )) or resi \ d 933 through 1065 or (resid 1066 and (name N or name CA or name C or name O or \ name CB )) or resid 1067 through 1148 or (resid 1149 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1150 through 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.600 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 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 : 0.002 0.042 28478 Z= 0.082 Angle : 0.396 8.690 38867 Z= 0.215 Chirality : 0.039 0.140 4389 Planarity : 0.003 0.049 4991 Dihedral : 7.746 87.803 10075 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.10 % Allowed : 4.57 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.12), residues: 3545 helix: 0.03 (0.18), residues: 751 sheet: -1.21 (0.18), residues: 670 loop : -2.89 (0.11), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 347 TYR 0.009 0.001 TYR A1148 PHE 0.007 0.001 PHE A 764 TRP 0.009 0.001 TRP A 344 HIS 0.002 0.000 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00161 (28405) covalent geometry : angle 0.39531 (38715) SS BOND : bond 0.00106 ( 67) SS BOND : angle 0.44077 ( 134) hydrogen bonds : bond 0.14389 ( 948) hydrogen bonds : angle 5.93161 ( 2757) link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.02929 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 570 time to evaluate : 0.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.6969 (mp) cc_final: 0.6598 (tt) REVERT: A 120 GLU cc_start: 0.5642 (mp0) cc_final: 0.5404 (mp0) REVERT: A 132 ASN cc_start: 0.7664 (p0) cc_final: 0.7424 (p0) REVERT: A 155 MET cc_start: 0.3566 (mmm) cc_final: 0.3173 (mmm) REVERT: A 218 MET cc_start: 0.6466 (ttm) cc_final: 0.6191 (ttm) REVERT: A 236 TYR cc_start: 0.6775 (t80) cc_final: 0.6213 (t80) REVERT: A 287 LEU cc_start: 0.7732 (tp) cc_final: 0.6978 (tp) REVERT: A 387 THR cc_start: 0.2791 (OUTLIER) cc_final: 0.2182 (p) REVERT: A 623 ASP cc_start: 0.6415 (t0) cc_final: 0.5955 (t0) REVERT: A 648 LEU cc_start: 0.7258 (tp) cc_final: 0.6054 (tp) REVERT: A 922 TYR cc_start: 0.7417 (m-80) cc_final: 0.7141 (m-80) REVERT: A 994 MET cc_start: 0.5597 (tpt) cc_final: 0.5174 (tpt) REVERT: A 1015 ILE cc_start: 0.6578 (tt) cc_final: 0.5432 (mt) REVERT: A 1036 ASN cc_start: 0.7748 (t0) cc_final: 0.7438 (t0) REVERT: A 1042 SER cc_start: 0.6952 (m) cc_final: 0.6625 (p) REVERT: A 1049 ASN cc_start: 0.8163 (m-40) cc_final: 0.7922 (m110) REVERT: A 1081 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7357 (ttm170) REVERT: A 1100 LYS cc_start: 0.6756 (mmmm) cc_final: 0.6553 (tppt) REVERT: A 1115 LYS cc_start: 0.4605 (OUTLIER) cc_final: 0.4205 (ttmm) REVERT: C 215 ASP cc_start: 0.4671 (p0) cc_final: 0.3083 (t0) REVERT: C 238 MET cc_start: 0.3222 (ptt) cc_final: 0.2901 (ptt) REVERT: C 448 TYR cc_start: 0.6215 (m-80) cc_final: 0.5774 (m-80) REVERT: C 615 SER cc_start: 0.7616 (m) cc_final: 0.7295 (t) REVERT: C 634 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6024 (mttp) REVERT: C 656 ILE cc_start: 0.6345 (pt) cc_final: 0.5967 (mt) REVERT: C 734 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6624 (m) REVERT: C 812 ILE cc_start: 0.8468 (mt) cc_final: 0.8219 (mm) REVERT: C 821 ASN cc_start: 0.7051 (m-40) cc_final: 0.6719 (m-40) REVERT: C 822 TYR cc_start: 0.6064 (m-80) cc_final: 0.5758 (m-80) REVERT: C 857 VAL cc_start: 0.7790 (t) cc_final: 0.7356 (m) REVERT: C 888 LEU cc_start: 0.7358 (mt) cc_final: 0.7137 (mt) REVERT: C 977 VAL cc_start: 0.6889 (t) cc_final: 0.6020 (m) REVERT: C 994 MET cc_start: 0.6719 (tpp) cc_final: 0.6169 (tpp) REVERT: C 1030 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6622 (mm110) REVERT: C 1034 ASN cc_start: 0.8047 (m-40) cc_final: 0.7738 (m-40) REVERT: C 1036 ASN cc_start: 0.7865 (m-40) cc_final: 0.7177 (t160) REVERT: C 1075 ASP cc_start: 0.6717 (m-30) cc_final: 0.5880 (m-30) REVERT: C 1094 SER cc_start: 0.7415 (m) cc_final: 0.6841 (t) REVERT: C 1096 ILE cc_start: 0.8239 (tp) cc_final: 0.7950 (tp) REVERT: C 1129 HIS cc_start: 0.5244 (t-90) cc_final: 0.5036 (t-90) REVERT: C 1180 GLN cc_start: 0.2812 (OUTLIER) cc_final: 0.2573 (tm130) REVERT: B 42 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7138 (t) REVERT: B 155 MET cc_start: 0.4542 (mmm) cc_final: 0.4104 (mmm) REVERT: B 209 PHE cc_start: 0.6881 (t80) cc_final: 0.3944 (t80) REVERT: B 266 TYR cc_start: 0.7661 (m-80) cc_final: 0.7025 (m-80) REVERT: B 289 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 615 SER cc_start: 0.8611 (t) cc_final: 0.8384 (p) REVERT: B 674 SER cc_start: 0.7641 (t) cc_final: 0.7422 (t) REVERT: B 676 ARG cc_start: 0.5821 (ttp80) cc_final: 0.5423 (mtp-110) REVERT: B 862 MET cc_start: 0.7304 (mtp) cc_final: 0.7050 (mtt) REVERT: B 949 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7046 (tp) REVERT: B 1043 LEU cc_start: 0.8275 (tp) cc_final: 0.7834 (tt) REVERT: B 1049 ASN cc_start: 0.7684 (m110) cc_final: 0.7368 (m110) REVERT: B 1057 SER cc_start: 0.8732 (t) cc_final: 0.8427 (p) REVERT: B 1060 GLU cc_start: 0.6893 (tt0) cc_final: 0.6524 (tt0) REVERT: B 1073 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7197 (mp10) REVERT: B 1110 VAL cc_start: 0.4644 (t) cc_final: 0.3344 (m) REVERT: B 1214 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6786 (tmtm) outliers start: 97 outliers final: 34 residues processed: 643 average time/residue: 0.1692 time to fit residues: 175.1419 Evaluate side-chains 480 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 437 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 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 19 ASN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 291 GLN A 433 ASN A 605 ASN A 709 GLN A 722 ASN A 789 GLN A 804 GLN A 821 ASN A 874 ASN A 876 HIS ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1201 ASN C 19 ASN C 248 ASN C 291 GLN C 410 GLN C 595 ASN C 683 GLN C 684 ASN C 789 GLN C 941 ASN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 GLN C1091 GLN C1180 GLN C1201 ASN B 160 HIS B 204 GLN B 243 ASN B 265 GLN B 402 GLN B 410 GLN B 445 ASN B 789 GLN B 821 ASN B 988 ASN B1001 GLN B1036 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.234622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194233 restraints weight = 65074.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.200824 restraints weight = 36179.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.202720 restraints weight = 21617.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.204918 restraints weight = 15339.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.204676 restraints weight = 13186.119| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28478 Z= 0.164 Angle : 0.583 12.370 38867 Z= 0.300 Chirality : 0.045 0.551 4389 Planarity : 0.004 0.051 4991 Dihedral : 5.165 59.717 4044 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.84 % Allowed : 9.30 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.13), residues: 3545 helix: 0.74 (0.19), residues: 747 sheet: -0.75 (0.19), residues: 669 loop : -2.52 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 986 TYR 0.036 0.002 TYR B1193 PHE 0.026 0.001 PHE C 473 TRP 0.026 0.001 TRP C 971 HIS 0.008 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00344 (28405) covalent geometry : angle 0.57591 (38715) SS BOND : bond 0.00286 ( 67) SS BOND : angle 1.10752 ( 134) hydrogen bonds : bond 0.03899 ( 948) hydrogen bonds : angle 4.87687 ( 2757) link_NAG-ASN : bond 0.00483 ( 6) link_NAG-ASN : angle 3.48554 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 482 time to evaluate : 1.061 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: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.6314 (ttm-80) cc_final: 0.6076 (ttm170) REVERT: A 120 GLU cc_start: 0.5366 (mp0) cc_final: 0.5135 (mm-30) REVERT: A 132 ASN cc_start: 0.7767 (p0) cc_final: 0.7543 (p0) REVERT: A 155 MET cc_start: 0.3968 (mmm) cc_final: 0.3520 (mmm) REVERT: A 218 MET cc_start: 0.6594 (ttm) cc_final: 0.6247 (ttm) REVERT: A 236 TYR cc_start: 0.6810 (t80) cc_final: 0.6196 (t80) REVERT: A 287 LEU cc_start: 0.7949 (tp) cc_final: 0.7651 (tp) REVERT: A 387 THR cc_start: 0.2826 (OUTLIER) cc_final: 0.2253 (p) REVERT: A 623 ASP cc_start: 0.6155 (t0) cc_final: 0.5727 (t0) REVERT: A 624 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4845 (pp) REVERT: A 646 ASN cc_start: 0.5272 (m-40) cc_final: 0.4998 (m-40) REVERT: A 683 GLN cc_start: 0.5598 (tm-30) cc_final: 0.5351 (tm-30) REVERT: A 780 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.5109 (mp0) REVERT: A 794 PHE cc_start: 0.6677 (p90) cc_final: 0.6258 (p90) REVERT: A 795 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7538 (t) REVERT: A 813 ASP cc_start: 0.6641 (t0) cc_final: 0.6219 (t0) REVERT: A 822 TYR cc_start: 0.6806 (m-80) cc_final: 0.6595 (m-80) REVERT: A 827 ASP cc_start: 0.7034 (m-30) cc_final: 0.6809 (m-30) REVERT: A 994 MET cc_start: 0.5499 (tpt) cc_final: 0.4761 (tpt) REVERT: A 1036 ASN cc_start: 0.7850 (t0) cc_final: 0.7572 (t0) REVERT: A 1042 SER cc_start: 0.7399 (m) cc_final: 0.7084 (p) REVERT: A 1061 ILE cc_start: 0.8702 (mt) cc_final: 0.8478 (mt) REVERT: A 1115 LYS cc_start: 0.4879 (OUTLIER) cc_final: 0.4100 (mttm) REVERT: A 1205 MET cc_start: 0.6510 (ttp) cc_final: 0.6276 (ttp) REVERT: C 155 MET cc_start: 0.4676 (mmm) cc_final: 0.3791 (mmm) REVERT: C 174 TRP cc_start: 0.6771 (p-90) cc_final: 0.6255 (p-90) REVERT: C 615 SER cc_start: 0.8081 (m) cc_final: 0.7375 (t) REVERT: C 624 LEU cc_start: 0.7630 (pp) cc_final: 0.7313 (pt) REVERT: C 634 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5925 (tttt) REVERT: C 821 ASN cc_start: 0.7155 (m-40) cc_final: 0.6856 (m-40) REVERT: C 822 TYR cc_start: 0.6151 (m-80) cc_final: 0.5787 (m-80) REVERT: C 840 ASN cc_start: 0.8012 (m110) cc_final: 0.7778 (m-40) REVERT: C 843 LEU cc_start: 0.8827 (mt) cc_final: 0.8550 (mp) REVERT: C 977 VAL cc_start: 0.7143 (t) cc_final: 0.6233 (m) REVERT: C 994 MET cc_start: 0.6849 (tpp) cc_final: 0.6059 (tpp) REVERT: C 1036 ASN cc_start: 0.7857 (m-40) cc_final: 0.7308 (t0) REVERT: C 1041 ASN cc_start: 0.7528 (m-40) cc_final: 0.7280 (m-40) REVERT: C 1071 GLN cc_start: 0.7545 (mm110) cc_final: 0.6570 (mm110) REVERT: C 1075 ASP cc_start: 0.7089 (m-30) cc_final: 0.6597 (m-30) REVERT: C 1079 ASN cc_start: 0.7651 (m110) cc_final: 0.7441 (m110) REVERT: C 1094 SER cc_start: 0.7765 (m) cc_final: 0.7148 (t) REVERT: C 1096 ILE cc_start: 0.8368 (tp) cc_final: 0.8090 (tp) REVERT: C 1129 HIS cc_start: 0.5750 (t-90) cc_final: 0.5527 (t-90) REVERT: B 42 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7209 (t) REVERT: B 155 MET cc_start: 0.5475 (mmm) cc_final: 0.4269 (mmm) REVERT: B 257 TRP cc_start: 0.6967 (m100) cc_final: 0.6238 (m100) REVERT: B 272 GLU cc_start: 0.7460 (pp20) cc_final: 0.7209 (pp20) REVERT: B 293 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7791 (ttmm) REVERT: B 641 TYR cc_start: 0.8015 (m-80) cc_final: 0.7796 (m-80) REVERT: B 674 SER cc_start: 0.7916 (t) cc_final: 0.7482 (p) REVERT: B 731 VAL cc_start: 0.7279 (p) cc_final: 0.6945 (t) REVERT: B 813 ASP cc_start: 0.6586 (p0) cc_final: 0.5746 (p0) REVERT: B 949 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7160 (tp) REVERT: B 1015 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7138 (tt) REVERT: B 1059 GLN cc_start: 0.7368 (tp40) cc_final: 0.7065 (tp-100) REVERT: B 1064 ARG cc_start: 0.6895 (mtm110) cc_final: 0.6481 (mtm110) REVERT: B 1073 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6993 (mp10) REVERT: B 1076 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7467 (ttm-80) REVERT: B 1099 ILE cc_start: 0.8245 (tt) cc_final: 0.7833 (pt) REVERT: B 1110 VAL cc_start: 0.4202 (t) cc_final: 0.2998 (m) REVERT: B 1195 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5783 (mm-30) REVERT: B 1205 MET cc_start: 0.3166 (mpp) cc_final: 0.2788 (mpp) REVERT: B 1214 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6733 (tmtm) outliers start: 89 outliers final: 53 residues processed: 540 average time/residue: 0.1821 time to fit residues: 159.2304 Evaluate side-chains 498 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 435 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 308 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 245 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 161 optimal weight: 0.0470 chunk 42 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 821 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.235076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.195134 restraints weight = 64654.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.201833 restraints weight = 36332.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.203670 restraints weight = 19167.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.205194 restraints weight = 14893.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.205032 restraints weight = 14864.678| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28478 Z= 0.111 Angle : 0.520 14.585 38867 Z= 0.266 Chirality : 0.043 0.354 4389 Planarity : 0.004 0.056 4991 Dihedral : 4.796 59.403 4030 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.19 % Allowed : 10.83 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.14), residues: 3545 helix: 1.00 (0.20), residues: 756 sheet: -0.52 (0.20), residues: 658 loop : -2.34 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.024 0.001 TYR B 699 PHE 0.019 0.001 PHE C1019 TRP 0.031 0.001 TRP C 971 HIS 0.003 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00244 (28405) covalent geometry : angle 0.51393 (38715) SS BOND : bond 0.00423 ( 67) SS BOND : angle 1.18970 ( 134) hydrogen bonds : bond 0.03498 ( 948) hydrogen bonds : angle 4.62652 ( 2757) link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 2.23446 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 445 time to evaluate : 1.183 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.5723 (mp0) cc_final: 0.5197 (mp0) REVERT: A 132 ASN cc_start: 0.7767 (p0) cc_final: 0.7542 (p0) REVERT: A 155 MET cc_start: 0.3783 (mmm) cc_final: 0.3319 (mmm) REVERT: A 186 LYS cc_start: 0.4854 (mmmm) cc_final: 0.4635 (mmmm) REVERT: A 213 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5631 (t80) REVERT: A 218 MET cc_start: 0.6581 (ttm) cc_final: 0.6268 (ttm) REVERT: A 236 TYR cc_start: 0.6766 (t80) cc_final: 0.6183 (t80) REVERT: A 287 LEU cc_start: 0.7933 (tp) cc_final: 0.7671 (tp) REVERT: A 387 THR cc_start: 0.2836 (OUTLIER) cc_final: 0.2263 (p) REVERT: A 623 ASP cc_start: 0.6029 (t0) cc_final: 0.5654 (t0) REVERT: A 624 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4909 (pp) REVERT: A 646 ASN cc_start: 0.5209 (m-40) cc_final: 0.4756 (m-40) REVERT: A 648 LEU cc_start: 0.7187 (tp) cc_final: 0.6986 (tp) REVERT: A 683 GLN cc_start: 0.5722 (tm-30) cc_final: 0.5434 (tm-30) REVERT: A 702 ASN cc_start: 0.7395 (t0) cc_final: 0.7038 (t0) REVERT: A 780 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5147 (mp0) REVERT: A 794 PHE cc_start: 0.6646 (p90) cc_final: 0.6188 (p90) REVERT: A 795 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7589 (t) REVERT: A 822 TYR cc_start: 0.6958 (m-80) cc_final: 0.6588 (m-80) REVERT: A 827 ASP cc_start: 0.6983 (m-30) cc_final: 0.6779 (m-30) REVERT: A 994 MET cc_start: 0.5537 (tpt) cc_final: 0.4769 (tpt) REVERT: A 1036 ASN cc_start: 0.7878 (t0) cc_final: 0.7566 (t0) REVERT: A 1042 SER cc_start: 0.7491 (m) cc_final: 0.7092 (p) REVERT: A 1055 SER cc_start: 0.8528 (p) cc_final: 0.8220 (m) REVERT: A 1061 ILE cc_start: 0.8729 (mt) cc_final: 0.8505 (mt) REVERT: A 1205 MET cc_start: 0.6561 (ttp) cc_final: 0.6302 (ttp) REVERT: C 155 MET cc_start: 0.4645 (mmm) cc_final: 0.3741 (mmm) REVERT: C 203 TYR cc_start: 0.6549 (p90) cc_final: 0.6348 (p90) REVERT: C 615 SER cc_start: 0.8078 (m) cc_final: 0.7344 (t) REVERT: C 634 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.5979 (ttmt) REVERT: C 821 ASN cc_start: 0.7186 (m-40) cc_final: 0.6869 (m-40) REVERT: C 822 TYR cc_start: 0.6208 (m-80) cc_final: 0.5743 (m-80) REVERT: C 922 TYR cc_start: 0.7786 (m-10) cc_final: 0.7547 (m-10) REVERT: C 977 VAL cc_start: 0.7209 (t) cc_final: 0.6345 (m) REVERT: C 994 MET cc_start: 0.6862 (tpp) cc_final: 0.6121 (tpp) REVERT: C 1036 ASN cc_start: 0.7923 (m-40) cc_final: 0.7273 (t0) REVERT: C 1041 ASN cc_start: 0.7561 (m-40) cc_final: 0.7278 (m-40) REVERT: C 1043 LEU cc_start: 0.7997 (pp) cc_final: 0.7600 (tp) REVERT: C 1060 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6948 (tt0) REVERT: C 1071 GLN cc_start: 0.7643 (mm110) cc_final: 0.6755 (mm110) REVERT: C 1075 ASP cc_start: 0.7354 (m-30) cc_final: 0.6799 (m-30) REVERT: C 1094 SER cc_start: 0.7780 (m) cc_final: 0.7176 (t) REVERT: C 1096 ILE cc_start: 0.8343 (tp) cc_final: 0.8076 (tp) REVERT: C 1129 HIS cc_start: 0.5795 (t-90) cc_final: 0.5545 (t-90) REVERT: B 42 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7261 (t) REVERT: B 56 TYR cc_start: 0.7499 (m-80) cc_final: 0.6762 (m-80) REVERT: B 155 MET cc_start: 0.5379 (mmm) cc_final: 0.4189 (mmm) REVERT: B 157 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7546 (tp30) REVERT: B 289 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 293 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7689 (ptpt) REVERT: B 635 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6626 (tm-30) REVERT: B 674 SER cc_start: 0.7970 (t) cc_final: 0.7569 (p) REVERT: B 731 VAL cc_start: 0.7358 (p) cc_final: 0.7049 (t) REVERT: B 813 ASP cc_start: 0.6403 (p0) cc_final: 0.6047 (p0) REVERT: B 839 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 949 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7110 (tp) REVERT: B 1015 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7131 (tt) REVERT: B 1043 LEU cc_start: 0.8211 (tp) cc_final: 0.7776 (tt) REVERT: B 1059 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6896 (tp-100) REVERT: B 1060 GLU cc_start: 0.6993 (tt0) cc_final: 0.6204 (tt0) REVERT: B 1064 ARG cc_start: 0.6863 (mtm110) cc_final: 0.6499 (mtm110) REVERT: B 1073 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6929 (mp10) REVERT: B 1099 ILE cc_start: 0.8247 (tt) cc_final: 0.7948 (pt) REVERT: B 1110 VAL cc_start: 0.4102 (t) cc_final: 0.2913 (m) REVERT: B 1195 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6133 (mm-30) REVERT: B 1214 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6743 (tmtm) outliers start: 100 outliers final: 63 residues processed: 502 average time/residue: 0.1795 time to fit residues: 146.0880 Evaluate side-chains 499 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 425 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 82 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 323 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 938 GLN A1000 ASN C 19 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 483 ASN B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.230330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.188800 restraints weight = 62703.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.195015 restraints weight = 34735.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.198931 restraints weight = 19642.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.198996 restraints weight = 15321.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.199344 restraints weight = 13053.458| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28478 Z= 0.212 Angle : 0.626 15.986 38867 Z= 0.329 Chirality : 0.046 0.321 4389 Planarity : 0.005 0.054 4991 Dihedral : 5.301 59.917 4025 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.15 % Allowed : 11.37 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.13), residues: 3545 helix: 0.57 (0.19), residues: 753 sheet: -0.66 (0.20), residues: 695 loop : -2.36 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 264 TYR 0.043 0.002 TYR C1139 PHE 0.042 0.002 PHE C1143 TRP 0.041 0.002 TRP C 444 HIS 0.007 0.001 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00449 (28405) covalent geometry : angle 0.62203 (38715) SS BOND : bond 0.00445 ( 67) SS BOND : angle 1.18550 ( 134) hydrogen bonds : bond 0.04754 ( 948) hydrogen bonds : angle 5.16557 ( 2757) link_NAG-ASN : bond 0.00453 ( 6) link_NAG-ASN : angle 2.02178 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 460 time to evaluate : 1.058 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7310 (ttpt) REVERT: A 186 LYS cc_start: 0.5308 (mmmm) cc_final: 0.5046 (mmmm) REVERT: A 213 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.6100 (t80) REVERT: A 218 MET cc_start: 0.6736 (ttm) cc_final: 0.6365 (ttm) REVERT: A 236 TYR cc_start: 0.7004 (t80) cc_final: 0.6446 (t80) REVERT: A 287 LEU cc_start: 0.8226 (tp) cc_final: 0.8018 (tp) REVERT: A 387 THR cc_start: 0.2984 (OUTLIER) cc_final: 0.2435 (p) REVERT: A 623 ASP cc_start: 0.5955 (t0) cc_final: 0.5751 (t0) REVERT: A 648 LEU cc_start: 0.7448 (tp) cc_final: 0.6847 (tp) REVERT: A 683 GLN cc_start: 0.5874 (tm-30) cc_final: 0.5585 (tm-30) REVERT: A 702 ASN cc_start: 0.7586 (t0) cc_final: 0.7251 (t0) REVERT: A 780 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5216 (mp0) REVERT: A 794 PHE cc_start: 0.6907 (p90) cc_final: 0.6504 (p90) REVERT: A 795 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 880 ASP cc_start: 0.2468 (OUTLIER) cc_final: 0.1513 (t0) REVERT: A 910 LYS cc_start: 0.4421 (mtpt) cc_final: 0.3493 (ttpp) REVERT: A 916 VAL cc_start: 0.2756 (OUTLIER) cc_final: 0.2371 (p) REVERT: A 922 TYR cc_start: 0.7738 (m-80) cc_final: 0.7414 (m-80) REVERT: A 943 ILE cc_start: 0.7602 (mt) cc_final: 0.7284 (mt) REVERT: A 994 MET cc_start: 0.5450 (tpt) cc_final: 0.5003 (tpt) REVERT: A 1036 ASN cc_start: 0.7917 (t0) cc_final: 0.7642 (t0) REVERT: A 1042 SER cc_start: 0.7614 (m) cc_final: 0.7246 (p) REVERT: A 1055 SER cc_start: 0.8573 (p) cc_final: 0.8259 (m) REVERT: A 1061 ILE cc_start: 0.8893 (mt) cc_final: 0.8637 (mt) REVERT: A 1205 MET cc_start: 0.6914 (ttp) cc_final: 0.6667 (ttp) REVERT: C 55 VAL cc_start: 0.6729 (OUTLIER) cc_final: 0.6464 (m) REVERT: C 155 MET cc_start: 0.4776 (mmm) cc_final: 0.4192 (mmm) REVERT: C 174 TRP cc_start: 0.7098 (p-90) cc_final: 0.6467 (p-90) REVERT: C 615 SER cc_start: 0.8125 (m) cc_final: 0.7389 (t) REVERT: C 647 LEU cc_start: 0.7796 (mt) cc_final: 0.7545 (mp) REVERT: C 651 SER cc_start: 0.9051 (m) cc_final: 0.8726 (p) REVERT: C 821 ASN cc_start: 0.7217 (m-40) cc_final: 0.6828 (m-40) REVERT: C 828 LEU cc_start: 0.8147 (tp) cc_final: 0.7665 (tt) REVERT: C 922 TYR cc_start: 0.7867 (m-10) cc_final: 0.7464 (m-10) REVERT: C 977 VAL cc_start: 0.7385 (t) cc_final: 0.6501 (m) REVERT: C 994 MET cc_start: 0.7080 (tpp) cc_final: 0.6342 (tpp) REVERT: C 1041 ASN cc_start: 0.7541 (m-40) cc_final: 0.7304 (m-40) REVERT: C 1060 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6907 (tt0) REVERT: C 1071 GLN cc_start: 0.7865 (mm110) cc_final: 0.7314 (mm110) REVERT: C 1075 ASP cc_start: 0.7505 (m-30) cc_final: 0.7017 (m-30) REVERT: C 1094 SER cc_start: 0.7951 (m) cc_final: 0.7356 (t) REVERT: C 1096 ILE cc_start: 0.8411 (tp) cc_final: 0.8147 (tp) REVERT: C 1191 TYR cc_start: 0.5925 (t80) cc_final: 0.5167 (t80) REVERT: B 56 TYR cc_start: 0.7587 (m-80) cc_final: 0.6890 (m-80) REVERT: B 60 THR cc_start: 0.7782 (p) cc_final: 0.7546 (p) REVERT: B 155 MET cc_start: 0.5395 (mmm) cc_final: 0.4676 (mmm) REVERT: B 635 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6505 (tm-30) REVERT: B 659 LYS cc_start: 0.7511 (tttt) cc_final: 0.7309 (mttt) REVERT: B 674 SER cc_start: 0.8031 (t) cc_final: 0.7708 (p) REVERT: B 731 VAL cc_start: 0.7322 (p) cc_final: 0.7038 (t) REVERT: B 806 SER cc_start: 0.7725 (t) cc_final: 0.7360 (m) REVERT: B 813 ASP cc_start: 0.6384 (p0) cc_final: 0.5813 (p0) REVERT: B 938 GLN cc_start: 0.7875 (mt0) cc_final: 0.7658 (tt0) REVERT: B 949 ILE cc_start: 0.7652 (pt) cc_final: 0.7211 (tp) REVERT: B 1015 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7221 (tt) REVERT: B 1059 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7124 (tp-100) REVERT: B 1073 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6955 (mp10) REVERT: B 1077 LEU cc_start: 0.8876 (mt) cc_final: 0.8533 (mp) REVERT: B 1195 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6135 (mm-30) REVERT: B 1205 MET cc_start: 0.3239 (mpp) cc_final: 0.2860 (mpp) REVERT: B 1214 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6693 (tmtm) outliers start: 130 outliers final: 72 residues processed: 546 average time/residue: 0.1768 time to fit residues: 157.7212 Evaluate side-chains 504 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 423 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1177 PHE Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 951 SER Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 256 optimal weight: 0.5980 chunk 170 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 342 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 331 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 703 ASN A 847 ASN A 941 ASN A 982 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.231188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.189617 restraints weight = 63561.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.196364 restraints weight = 34983.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.198361 restraints weight = 21709.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.201499 restraints weight = 14629.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.201113 restraints weight = 12045.940| |-----------------------------------------------------------------------------| r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28478 Z= 0.131 Angle : 0.560 16.040 38867 Z= 0.290 Chirality : 0.044 0.277 4389 Planarity : 0.004 0.056 4991 Dihedral : 4.942 58.730 4011 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.16 % Allowed : 13.55 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.14), residues: 3545 helix: 0.92 (0.20), residues: 743 sheet: -0.54 (0.20), residues: 688 loop : -2.25 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1120 TYR 0.031 0.001 TYR C 266 PHE 0.026 0.001 PHE C 67 TRP 0.050 0.002 TRP C 444 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00289 (28405) covalent geometry : angle 0.55447 (38715) SS BOND : bond 0.00307 ( 67) SS BOND : angle 1.31479 ( 134) hydrogen bonds : bond 0.03963 ( 948) hydrogen bonds : angle 4.93684 ( 2757) link_NAG-ASN : bond 0.00352 ( 6) link_NAG-ASN : angle 1.90256 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 437 time to evaluate : 1.030 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7196 (ttpt) REVERT: A 155 MET cc_start: 0.4209 (mmm) cc_final: 0.3999 (mmm) REVERT: A 186 LYS cc_start: 0.5252 (mmmm) cc_final: 0.4980 (mmmm) REVERT: A 213 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5853 (t80) REVERT: A 218 MET cc_start: 0.6723 (ttm) cc_final: 0.6341 (ttm) REVERT: A 236 TYR cc_start: 0.6946 (t80) cc_final: 0.6437 (t80) REVERT: A 287 LEU cc_start: 0.8149 (tp) cc_final: 0.7947 (tp) REVERT: A 387 THR cc_start: 0.2869 (OUTLIER) cc_final: 0.2327 (p) REVERT: A 623 ASP cc_start: 0.6057 (t0) cc_final: 0.5805 (t0) REVERT: A 624 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5223 (pp) REVERT: A 683 GLN cc_start: 0.5968 (tm-30) cc_final: 0.5693 (tm-30) REVERT: A 702 ASN cc_start: 0.7532 (t0) cc_final: 0.7202 (t0) REVERT: A 746 TYR cc_start: 0.6223 (t80) cc_final: 0.5865 (t80) REVERT: A 780 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5118 (mp0) REVERT: A 794 PHE cc_start: 0.6767 (p90) cc_final: 0.6354 (p90) REVERT: A 795 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7918 (t) REVERT: A 880 ASP cc_start: 0.2569 (OUTLIER) cc_final: 0.1538 (t0) REVERT: A 910 LYS cc_start: 0.4467 (mtpt) cc_final: 0.3556 (ttpp) REVERT: A 916 VAL cc_start: 0.3092 (OUTLIER) cc_final: 0.2676 (p) REVERT: A 922 TYR cc_start: 0.7584 (m-80) cc_final: 0.7281 (m-80) REVERT: A 943 ILE cc_start: 0.7500 (mt) cc_final: 0.7126 (mt) REVERT: A 994 MET cc_start: 0.5372 (tpt) cc_final: 0.4966 (tpt) REVERT: A 1036 ASN cc_start: 0.7866 (t0) cc_final: 0.7547 (t0) REVERT: A 1042 SER cc_start: 0.7546 (m) cc_final: 0.7182 (p) REVERT: A 1061 ILE cc_start: 0.8804 (mt) cc_final: 0.8598 (mt) REVERT: A 1076 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7674 (mtp85) REVERT: A 1205 MET cc_start: 0.6872 (ttp) cc_final: 0.6635 (ttp) REVERT: C 155 MET cc_start: 0.4596 (mmm) cc_final: 0.4026 (mmm) REVERT: C 174 TRP cc_start: 0.7022 (p-90) cc_final: 0.6443 (p-90) REVERT: C 238 MET cc_start: 0.3463 (ptt) cc_final: 0.3028 (ptt) REVERT: C 266 TYR cc_start: 0.6838 (m-80) cc_final: 0.5596 (m-80) REVERT: C 281 ASP cc_start: 0.6261 (m-30) cc_final: 0.5720 (t70) REVERT: C 615 SER cc_start: 0.8185 (m) cc_final: 0.7422 (t) REVERT: C 623 ASP cc_start: 0.6992 (t0) cc_final: 0.6280 (t0) REVERT: C 647 LEU cc_start: 0.7498 (mt) cc_final: 0.7093 (mp) REVERT: C 651 SER cc_start: 0.9051 (m) cc_final: 0.8726 (p) REVERT: C 821 ASN cc_start: 0.7258 (m-40) cc_final: 0.6885 (m-40) REVERT: C 822 TYR cc_start: 0.6569 (m-80) cc_final: 0.5784 (m-80) REVERT: C 828 LEU cc_start: 0.8157 (tp) cc_final: 0.7614 (tt) REVERT: C 857 VAL cc_start: 0.8028 (t) cc_final: 0.7524 (m) REVERT: C 922 TYR cc_start: 0.7851 (m-10) cc_final: 0.7442 (m-10) REVERT: C 977 VAL cc_start: 0.7400 (t) cc_final: 0.6596 (m) REVERT: C 994 MET cc_start: 0.7057 (tpp) cc_final: 0.6299 (tpp) REVERT: C 1060 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6853 (tt0) REVERT: C 1071 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7321 (mm-40) REVERT: C 1075 ASP cc_start: 0.7393 (m-30) cc_final: 0.6828 (m-30) REVERT: C 1094 SER cc_start: 0.7942 (m) cc_final: 0.7337 (t) REVERT: C 1096 ILE cc_start: 0.8383 (tp) cc_final: 0.8113 (tp) REVERT: B 56 TYR cc_start: 0.7598 (m-80) cc_final: 0.6809 (m-80) REVERT: B 155 MET cc_start: 0.5256 (mmm) cc_final: 0.4542 (mmm) REVERT: B 232 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7856 (tp) REVERT: B 264 ARG cc_start: 0.6876 (ptp-170) cc_final: 0.6463 (ptp90) REVERT: B 635 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6511 (tm-30) REVERT: B 674 SER cc_start: 0.7965 (t) cc_final: 0.7605 (p) REVERT: B 731 VAL cc_start: 0.7262 (p) cc_final: 0.7017 (t) REVERT: B 806 SER cc_start: 0.7598 (t) cc_final: 0.7256 (m) REVERT: B 813 ASP cc_start: 0.6063 (p0) cc_final: 0.5835 (p0) REVERT: B 933 ASP cc_start: 0.6426 (t70) cc_final: 0.6171 (t70) REVERT: B 934 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6652 (pp) REVERT: B 949 ILE cc_start: 0.7586 (pt) cc_final: 0.7130 (tp) REVERT: B 967 MET cc_start: 0.3780 (tpp) cc_final: 0.3554 (tpp) REVERT: B 1015 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7103 (tt) REVERT: B 1059 GLN cc_start: 0.7369 (tp-100) cc_final: 0.6981 (tp-100) REVERT: B 1077 LEU cc_start: 0.8849 (mt) cc_final: 0.8503 (mp) REVERT: B 1195 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6136 (mm-30) REVERT: B 1214 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6634 (tmtm) outliers start: 99 outliers final: 70 residues processed: 499 average time/residue: 0.1839 time to fit residues: 148.2918 Evaluate side-chains 498 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 417 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1177 PHE Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 16 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 354 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN B 243 ASN B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN B1206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.236597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.205425 restraints weight = 75467.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.206462 restraints weight = 46377.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.208331 restraints weight = 34211.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.208764 restraints weight = 25500.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.208921 restraints weight = 22830.276| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28478 Z= 0.173 Angle : 0.590 15.705 38867 Z= 0.309 Chirality : 0.045 0.282 4389 Planarity : 0.004 0.055 4991 Dihedral : 5.128 59.221 4011 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.67 % Allowed : 13.77 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.14), residues: 3545 helix: 0.80 (0.19), residues: 741 sheet: -0.62 (0.20), residues: 677 loop : -2.22 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1120 TYR 0.025 0.002 TYR B 203 PHE 0.028 0.002 PHE C1143 TRP 0.071 0.002 TRP C 444 HIS 0.011 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00372 (28405) covalent geometry : angle 0.58508 (38715) SS BOND : bond 0.00333 ( 67) SS BOND : angle 1.23882 ( 134) hydrogen bonds : bond 0.04356 ( 948) hydrogen bonds : angle 5.07376 ( 2757) link_NAG-ASN : bond 0.00380 ( 6) link_NAG-ASN : angle 1.96307 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 443 time to evaluate : 1.072 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7137 (ttpt) REVERT: A 155 MET cc_start: 0.4957 (mmm) cc_final: 0.4734 (mmm) REVERT: A 186 LYS cc_start: 0.5412 (mmmm) cc_final: 0.5084 (mmmm) REVERT: A 213 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5921 (t80) REVERT: A 218 MET cc_start: 0.6803 (ttm) cc_final: 0.6467 (ttm) REVERT: A 236 TYR cc_start: 0.6857 (t80) cc_final: 0.6288 (t80) REVERT: A 387 THR cc_start: 0.2847 (OUTLIER) cc_final: 0.2379 (p) REVERT: A 624 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5193 (pp) REVERT: A 683 GLN cc_start: 0.6021 (tm-30) cc_final: 0.5697 (tm-30) REVERT: A 702 ASN cc_start: 0.7673 (t0) cc_final: 0.7334 (t0) REVERT: A 746 TYR cc_start: 0.6469 (t80) cc_final: 0.5895 (t80) REVERT: A 780 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5443 (mp0) REVERT: A 794 PHE cc_start: 0.6918 (p90) cc_final: 0.6540 (p90) REVERT: A 795 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7975 (t) REVERT: A 880 ASP cc_start: 0.2319 (OUTLIER) cc_final: 0.1320 (t0) REVERT: A 910 LYS cc_start: 0.4616 (mtpt) cc_final: 0.3579 (mtpp) REVERT: A 922 TYR cc_start: 0.7744 (m-80) cc_final: 0.7381 (m-80) REVERT: A 943 ILE cc_start: 0.7512 (mt) cc_final: 0.7186 (mt) REVERT: A 994 MET cc_start: 0.5467 (tpt) cc_final: 0.5046 (tpt) REVERT: A 1028 LYS cc_start: 0.6749 (mptm) cc_final: 0.6180 (mptm) REVERT: A 1036 ASN cc_start: 0.7874 (t0) cc_final: 0.7552 (t0) REVERT: A 1042 SER cc_start: 0.7677 (m) cc_final: 0.7311 (p) REVERT: A 1100 LYS cc_start: 0.6915 (tppt) cc_final: 0.6711 (tppt) REVERT: A 1115 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5005 (mttm) REVERT: A 1120 ARG cc_start: 0.5728 (tpp80) cc_final: 0.4903 (mmp-170) REVERT: A 1205 MET cc_start: 0.7029 (ttp) cc_final: 0.6694 (ttp) REVERT: C 174 TRP cc_start: 0.7083 (p-90) cc_final: 0.6644 (p-90) REVERT: C 266 TYR cc_start: 0.6878 (m-80) cc_final: 0.5742 (m-80) REVERT: C 281 ASP cc_start: 0.6261 (m-30) cc_final: 0.5787 (t70) REVERT: C 615 SER cc_start: 0.8146 (m) cc_final: 0.7427 (t) REVERT: C 623 ASP cc_start: 0.7010 (t0) cc_final: 0.6336 (t0) REVERT: C 646 ASN cc_start: 0.7248 (t0) cc_final: 0.6952 (t0) REVERT: C 647 LEU cc_start: 0.7618 (mt) cc_final: 0.7255 (mp) REVERT: C 651 SER cc_start: 0.9060 (m) cc_final: 0.8801 (p) REVERT: C 821 ASN cc_start: 0.7266 (m-40) cc_final: 0.6830 (m-40) REVERT: C 828 LEU cc_start: 0.8168 (tp) cc_final: 0.7515 (tt) REVERT: C 977 VAL cc_start: 0.7316 (t) cc_final: 0.6470 (m) REVERT: C 994 MET cc_start: 0.7127 (tpp) cc_final: 0.6364 (tpp) REVERT: C 1026 LEU cc_start: 0.1600 (OUTLIER) cc_final: 0.0131 (tp) REVERT: C 1036 ASN cc_start: 0.7854 (m-40) cc_final: 0.7239 (t0) REVERT: C 1060 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6981 (tt0) REVERT: C 1071 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7525 (mm-40) REVERT: C 1075 ASP cc_start: 0.7611 (m-30) cc_final: 0.6916 (m-30) REVERT: C 1094 SER cc_start: 0.7965 (m) cc_final: 0.7370 (t) REVERT: B 56 TYR cc_start: 0.7652 (m-80) cc_final: 0.6984 (m-80) REVERT: B 89 TRP cc_start: 0.6493 (m-10) cc_final: 0.6278 (m-90) REVERT: B 120 GLU cc_start: 0.2272 (mp0) cc_final: 0.1870 (tt0) REVERT: B 155 MET cc_start: 0.6323 (mmm) cc_final: 0.5221 (mmm) REVERT: B 232 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (tp) REVERT: B 264 ARG cc_start: 0.6929 (ptp-170) cc_final: 0.6506 (ptp90) REVERT: B 635 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6637 (tm-30) REVERT: B 674 SER cc_start: 0.8056 (t) cc_final: 0.7775 (p) REVERT: B 731 VAL cc_start: 0.7290 (p) cc_final: 0.7057 (t) REVERT: B 806 SER cc_start: 0.7693 (t) cc_final: 0.7366 (m) REVERT: B 813 ASP cc_start: 0.6296 (p0) cc_final: 0.6053 (p0) REVERT: B 934 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6524 (pp) REVERT: B 949 ILE cc_start: 0.7564 (pt) cc_final: 0.7101 (tp) REVERT: B 967 MET cc_start: 0.3946 (tpp) cc_final: 0.3690 (tpp) REVERT: B 1015 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (tt) REVERT: B 1059 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7060 (tp-100) REVERT: B 1073 GLN cc_start: 0.7640 (mt0) cc_final: 0.7373 (mt0) REVERT: B 1077 LEU cc_start: 0.8815 (mt) cc_final: 0.8476 (mp) REVERT: B 1195 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6072 (mm-30) REVERT: B 1205 MET cc_start: 0.3242 (mpp) cc_final: 0.3017 (mpp) REVERT: B 1214 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6645 (tmtm) outliers start: 115 outliers final: 74 residues processed: 513 average time/residue: 0.1836 time to fit residues: 152.4668 Evaluate side-chains 511 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 425 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1177 PHE Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 697 CYS Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 133 optimal weight: 0.0070 chunk 263 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 344 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.230708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.189201 restraints weight = 62823.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.195919 restraints weight = 34328.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.197700 restraints weight = 21690.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.200850 restraints weight = 14815.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.200374 restraints weight = 12004.264| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28478 Z= 0.120 Angle : 0.551 16.063 38867 Z= 0.283 Chirality : 0.043 0.268 4389 Planarity : 0.004 0.056 4991 Dihedral : 4.959 56.129 4010 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.32 % Allowed : 14.82 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 3545 helix: 1.13 (0.20), residues: 740 sheet: -0.40 (0.20), residues: 663 loop : -2.14 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.023 0.001 TYR B 699 PHE 0.023 0.001 PHE B 368 TRP 0.067 0.002 TRP C 444 HIS 0.007 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00266 (28405) covalent geometry : angle 0.54728 (38715) SS BOND : bond 0.00264 ( 67) SS BOND : angle 1.08263 ( 134) hydrogen bonds : bond 0.03801 ( 948) hydrogen bonds : angle 4.84540 ( 2757) link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 1.85589 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 435 time to evaluate : 1.003 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: symmetry clash 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: symmetry clash REVERT: A 105 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7124 (ttpt) REVERT: A 186 LYS cc_start: 0.5202 (mmmm) cc_final: 0.4947 (mmmm) REVERT: A 213 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5762 (t80) REVERT: A 218 MET cc_start: 0.6791 (ttm) cc_final: 0.6367 (ttm) REVERT: A 236 TYR cc_start: 0.6912 (t80) cc_final: 0.6406 (t80) REVERT: A 287 LEU cc_start: 0.8125 (tp) cc_final: 0.7811 (tt) REVERT: A 387 THR cc_start: 0.2934 (OUTLIER) cc_final: 0.2421 (p) REVERT: A 624 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5266 (pp) REVERT: A 683 GLN cc_start: 0.6080 (tm-30) cc_final: 0.5737 (tm-30) REVERT: A 702 ASN cc_start: 0.7516 (t0) cc_final: 0.7180 (t0) REVERT: A 746 TYR cc_start: 0.6547 (t80) cc_final: 0.6037 (t80) REVERT: A 794 PHE cc_start: 0.6799 (p90) cc_final: 0.6374 (p90) REVERT: A 795 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7885 (t) REVERT: A 880 ASP cc_start: 0.2468 (OUTLIER) cc_final: 0.1407 (t0) REVERT: A 910 LYS cc_start: 0.4660 (mtpt) cc_final: 0.3636 (mtpp) REVERT: A 916 VAL cc_start: 0.2963 (OUTLIER) cc_final: 0.2539 (p) REVERT: A 922 TYR cc_start: 0.7605 (m-80) cc_final: 0.7283 (m-80) REVERT: A 943 ILE cc_start: 0.7485 (mt) cc_final: 0.7112 (mt) REVERT: A 994 MET cc_start: 0.5417 (tpt) cc_final: 0.5014 (tpt) REVERT: A 1028 LYS cc_start: 0.6772 (mptm) cc_final: 0.6171 (mptm) REVERT: A 1036 ASN cc_start: 0.7848 (t0) cc_final: 0.7505 (t0) REVERT: A 1042 SER cc_start: 0.7608 (m) cc_final: 0.7244 (p) REVERT: A 1076 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7847 (mtm-85) REVERT: A 1100 LYS cc_start: 0.6854 (tppt) cc_final: 0.6646 (tppt) REVERT: A 1205 MET cc_start: 0.6883 (ttp) cc_final: 0.6648 (ttp) REVERT: C 155 MET cc_start: 0.3921 (mmm) cc_final: 0.2963 (mmm) REVERT: C 174 TRP cc_start: 0.6870 (p-90) cc_final: 0.6270 (p-90) REVERT: C 266 TYR cc_start: 0.6847 (m-80) cc_final: 0.6095 (m-80) REVERT: C 281 ASP cc_start: 0.6337 (m-30) cc_final: 0.5778 (t0) REVERT: C 615 SER cc_start: 0.8152 (m) cc_final: 0.7432 (t) REVERT: C 623 ASP cc_start: 0.6989 (t0) cc_final: 0.6297 (t0) REVERT: C 646 ASN cc_start: 0.7236 (t0) cc_final: 0.6909 (t0) REVERT: C 647 LEU cc_start: 0.7508 (mt) cc_final: 0.7128 (mp) REVERT: C 651 SER cc_start: 0.9038 (m) cc_final: 0.8789 (p) REVERT: C 821 ASN cc_start: 0.7269 (m-40) cc_final: 0.6810 (m-40) REVERT: C 828 LEU cc_start: 0.8174 (tp) cc_final: 0.7496 (tp) REVERT: C 857 VAL cc_start: 0.7949 (t) cc_final: 0.7473 (m) REVERT: C 977 VAL cc_start: 0.7347 (t) cc_final: 0.6542 (m) REVERT: C 994 MET cc_start: 0.7077 (tpp) cc_final: 0.6351 (tpp) REVERT: C 1026 LEU cc_start: 0.1615 (OUTLIER) cc_final: 0.0205 (tp) REVERT: C 1036 ASN cc_start: 0.7852 (m-40) cc_final: 0.7186 (t0) REVERT: C 1060 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6912 (tt0) REVERT: C 1071 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7412 (mm110) REVERT: C 1075 ASP cc_start: 0.7437 (m-30) cc_final: 0.6784 (m-30) REVERT: C 1094 SER cc_start: 0.7996 (m) cc_final: 0.7391 (t) REVERT: C 1109 LYS cc_start: 0.3861 (OUTLIER) cc_final: 0.1706 (mttt) REVERT: C 1191 TYR cc_start: 0.5892 (t80) cc_final: 0.5145 (t80) REVERT: B 56 TYR cc_start: 0.7611 (m-80) cc_final: 0.6973 (m-80) REVERT: B 120 GLU cc_start: 0.2525 (mp0) cc_final: 0.2086 (tt0) REVERT: B 155 MET cc_start: 0.5475 (mmm) cc_final: 0.4669 (mmm) REVERT: B 635 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6449 (tm-30) REVERT: B 674 SER cc_start: 0.8001 (t) cc_final: 0.7682 (p) REVERT: B 806 SER cc_start: 0.7643 (t) cc_final: 0.7384 (m) REVERT: B 935 LEU cc_start: 0.7530 (mm) cc_final: 0.7272 (mm) REVERT: B 949 ILE cc_start: 0.7577 (pt) cc_final: 0.7089 (tp) REVERT: B 967 MET cc_start: 0.3739 (tpp) cc_final: 0.3535 (tpp) REVERT: B 1015 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7095 (tt) REVERT: B 1059 GLN cc_start: 0.7366 (tp-100) cc_final: 0.7120 (tp40) REVERT: B 1073 GLN cc_start: 0.7465 (mt0) cc_final: 0.7198 (mt0) REVERT: B 1077 LEU cc_start: 0.8885 (mt) cc_final: 0.8561 (mp) REVERT: B 1195 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6108 (mm-30) REVERT: B 1214 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6630 (tmtm) outliers start: 104 outliers final: 67 residues processed: 501 average time/residue: 0.1820 time to fit residues: 148.2539 Evaluate side-chains 497 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 420 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1000 ASN Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 96 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.231064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.189285 restraints weight = 63065.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.195742 restraints weight = 34833.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.197910 restraints weight = 21672.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.199457 restraints weight = 15182.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.199970 restraints weight = 13117.693| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28478 Z= 0.153 Angle : 0.584 15.666 38867 Z= 0.303 Chirality : 0.045 0.442 4389 Planarity : 0.004 0.064 4991 Dihedral : 5.125 57.383 4005 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.42 % Allowed : 14.98 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 3545 helix: 0.94 (0.19), residues: 746 sheet: -0.43 (0.20), residues: 664 loop : -2.13 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 676 TYR 0.025 0.001 TYR A 641 PHE 0.024 0.001 PHE B 368 TRP 0.054 0.002 TRP B 89 HIS 0.006 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00332 (28405) covalent geometry : angle 0.57995 (38715) SS BOND : bond 0.00299 ( 67) SS BOND : angle 1.08089 ( 134) hydrogen bonds : bond 0.04126 ( 948) hydrogen bonds : angle 4.96385 ( 2757) link_NAG-ASN : bond 0.00369 ( 6) link_NAG-ASN : angle 1.94588 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 437 time to evaluate : 0.847 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: 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 105 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7158 (ttpt) REVERT: A 186 LYS cc_start: 0.5308 (mmmm) cc_final: 0.5043 (mmmm) REVERT: A 213 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5861 (t80) REVERT: A 218 MET cc_start: 0.6798 (ttm) cc_final: 0.6418 (ttm) REVERT: A 236 TYR cc_start: 0.6939 (t80) cc_final: 0.6440 (t80) REVERT: A 287 LEU cc_start: 0.8232 (tp) cc_final: 0.7851 (tt) REVERT: A 387 THR cc_start: 0.3106 (OUTLIER) cc_final: 0.2586 (p) REVERT: A 624 LEU cc_start: 0.5601 (OUTLIER) cc_final: 0.5348 (pp) REVERT: A 683 GLN cc_start: 0.6146 (tm-30) cc_final: 0.5791 (tm-30) REVERT: A 702 ASN cc_start: 0.7516 (t0) cc_final: 0.7141 (t0) REVERT: A 746 TYR cc_start: 0.6737 (t80) cc_final: 0.6087 (t80) REVERT: A 780 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.5140 (mp0) REVERT: A 794 PHE cc_start: 0.6903 (p90) cc_final: 0.6516 (p90) REVERT: A 795 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7914 (t) REVERT: A 880 ASP cc_start: 0.2414 (OUTLIER) cc_final: 0.1362 (t0) REVERT: A 910 LYS cc_start: 0.4749 (mtpt) cc_final: 0.3716 (mtpp) REVERT: A 922 TYR cc_start: 0.7712 (m-80) cc_final: 0.7370 (m-80) REVERT: A 943 ILE cc_start: 0.7582 (mt) cc_final: 0.7225 (mt) REVERT: A 994 MET cc_start: 0.5462 (tpt) cc_final: 0.5040 (tpt) REVERT: A 1036 ASN cc_start: 0.7890 (t0) cc_final: 0.7559 (t0) REVERT: A 1042 SER cc_start: 0.7660 (m) cc_final: 0.7278 (p) REVERT: A 1120 ARG cc_start: 0.5692 (tpp80) cc_final: 0.4946 (mmp-170) REVERT: A 1205 MET cc_start: 0.6889 (ttp) cc_final: 0.6664 (ttp) REVERT: C 155 MET cc_start: 0.4081 (mmm) cc_final: 0.3255 (mmm) REVERT: C 174 TRP cc_start: 0.6772 (p-90) cc_final: 0.6178 (p-90) REVERT: C 203 TYR cc_start: 0.6445 (p90) cc_final: 0.5979 (p90) REVERT: C 281 ASP cc_start: 0.6356 (m-30) cc_final: 0.5812 (t70) REVERT: C 615 SER cc_start: 0.8169 (m) cc_final: 0.7445 (t) REVERT: C 623 ASP cc_start: 0.7035 (t0) cc_final: 0.6354 (t0) REVERT: C 646 ASN cc_start: 0.7282 (t0) cc_final: 0.6953 (t0) REVERT: C 647 LEU cc_start: 0.7581 (mt) cc_final: 0.7239 (mp) REVERT: C 652 ASN cc_start: 0.7292 (p0) cc_final: 0.6828 (p0) REVERT: C 821 ASN cc_start: 0.7238 (m-40) cc_final: 0.6869 (m110) REVERT: C 977 VAL cc_start: 0.7328 (t) cc_final: 0.6439 (m) REVERT: C 994 MET cc_start: 0.7181 (tpp) cc_final: 0.6494 (tpp) REVERT: C 1026 LEU cc_start: 0.1549 (OUTLIER) cc_final: 0.0106 (tp) REVERT: C 1036 ASN cc_start: 0.7852 (m-40) cc_final: 0.7199 (t0) REVERT: C 1060 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6970 (tt0) REVERT: C 1071 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7629 (mm110) REVERT: C 1094 SER cc_start: 0.7932 (m) cc_final: 0.7331 (t) REVERT: C 1109 LYS cc_start: 0.3859 (OUTLIER) cc_final: 0.3522 (ttmm) REVERT: C 1191 TYR cc_start: 0.5922 (t80) cc_final: 0.5150 (t80) REVERT: B 56 TYR cc_start: 0.7657 (m-80) cc_final: 0.7238 (m-80) REVERT: B 120 GLU cc_start: 0.2819 (mp0) cc_final: 0.2508 (tt0) REVERT: B 155 MET cc_start: 0.5649 (mmm) cc_final: 0.4784 (mmm) REVERT: B 232 LEU cc_start: 0.8056 (tp) cc_final: 0.7851 (tp) REVERT: B 264 ARG cc_start: 0.6892 (ptp-170) cc_final: 0.6465 (ptp90) REVERT: B 635 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6433 (tm-30) REVERT: B 674 SER cc_start: 0.7977 (t) cc_final: 0.7665 (p) REVERT: B 806 SER cc_start: 0.7726 (t) cc_final: 0.7480 (m) REVERT: B 809 LYS cc_start: 0.6403 (mttp) cc_final: 0.6142 (mttp) REVERT: B 820 SER cc_start: 0.7949 (t) cc_final: 0.7685 (m) REVERT: B 949 ILE cc_start: 0.7597 (pt) cc_final: 0.7133 (tp) REVERT: B 1015 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7167 (tt) REVERT: B 1059 GLN cc_start: 0.7439 (tp-100) cc_final: 0.6994 (tp-100) REVERT: B 1073 GLN cc_start: 0.7493 (mt0) cc_final: 0.7239 (mt0) REVERT: B 1077 LEU cc_start: 0.8882 (mt) cc_final: 0.8558 (mp) REVERT: B 1195 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6173 (mm-30) REVERT: B 1214 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6668 (tmtm) outliers start: 107 outliers final: 76 residues processed: 505 average time/residue: 0.1689 time to fit residues: 138.1221 Evaluate side-chains 510 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1177 PHE Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1209 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 160 optimal weight: 0.0570 chunk 164 optimal weight: 30.0000 chunk 352 optimal weight: 0.0570 chunk 325 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 277 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.231142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.189504 restraints weight = 63614.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.196399 restraints weight = 34987.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.198646 restraints weight = 21493.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.201351 restraints weight = 14445.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.201305 restraints weight = 11874.112| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28478 Z= 0.105 Angle : 0.571 14.222 38867 Z= 0.290 Chirality : 0.043 0.311 4389 Planarity : 0.004 0.084 4991 Dihedral : 4.839 58.169 4001 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.72 % Allowed : 15.72 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.14), residues: 3545 helix: 1.26 (0.20), residues: 742 sheet: -0.20 (0.21), residues: 647 loop : -2.05 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 34 TYR 0.024 0.001 TYR A 158 PHE 0.024 0.001 PHE B 368 TRP 0.052 0.002 TRP B 89 HIS 0.004 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00237 (28405) covalent geometry : angle 0.56836 (38715) SS BOND : bond 0.00228 ( 67) SS BOND : angle 0.94374 ( 134) hydrogen bonds : bond 0.03500 ( 948) hydrogen bonds : angle 4.73186 ( 2757) link_NAG-ASN : bond 0.00357 ( 6) link_NAG-ASN : angle 1.87956 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 425 time to evaluate : 1.027 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: 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 105 LYS cc_start: 0.7508 (ttpt) cc_final: 0.7081 (ttpt) REVERT: A 186 LYS cc_start: 0.5295 (mmmm) cc_final: 0.5004 (mmmm) REVERT: A 213 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5663 (t80) REVERT: A 218 MET cc_start: 0.6761 (ttm) cc_final: 0.6349 (ttm) REVERT: A 236 TYR cc_start: 0.6826 (t80) cc_final: 0.6331 (t80) REVERT: A 271 ASP cc_start: 0.7282 (p0) cc_final: 0.6916 (p0) REVERT: A 287 LEU cc_start: 0.8078 (tp) cc_final: 0.7696 (tt) REVERT: A 387 THR cc_start: 0.3071 (OUTLIER) cc_final: 0.2542 (p) REVERT: A 624 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5356 (pp) REVERT: A 683 GLN cc_start: 0.6118 (tm-30) cc_final: 0.5764 (tm-30) REVERT: A 702 ASN cc_start: 0.7439 (t0) cc_final: 0.7070 (t0) REVERT: A 746 TYR cc_start: 0.6706 (t80) cc_final: 0.6166 (t80) REVERT: A 780 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4988 (mp0) REVERT: A 794 PHE cc_start: 0.6752 (p90) cc_final: 0.6323 (p90) REVERT: A 795 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 880 ASP cc_start: 0.2369 (OUTLIER) cc_final: 0.1301 (t0) REVERT: A 910 LYS cc_start: 0.4619 (mtpt) cc_final: 0.3579 (tttm) REVERT: A 916 VAL cc_start: 0.2735 (OUTLIER) cc_final: 0.2262 (p) REVERT: A 922 TYR cc_start: 0.7561 (m-80) cc_final: 0.7219 (m-80) REVERT: A 943 ILE cc_start: 0.7381 (mt) cc_final: 0.7006 (mt) REVERT: A 994 MET cc_start: 0.5417 (tpt) cc_final: 0.5004 (tpt) REVERT: A 1033 VAL cc_start: 0.8303 (m) cc_final: 0.8079 (p) REVERT: A 1036 ASN cc_start: 0.7764 (t0) cc_final: 0.7410 (t0) REVERT: A 1042 SER cc_start: 0.7568 (m) cc_final: 0.7232 (p) REVERT: A 1115 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.4469 (mttm) REVERT: C 155 MET cc_start: 0.3687 (mmm) cc_final: 0.3068 (mmm) REVERT: C 174 TRP cc_start: 0.6703 (p-90) cc_final: 0.6116 (p-90) REVERT: C 203 TYR cc_start: 0.6386 (p90) cc_final: 0.5916 (p90) REVERT: C 266 TYR cc_start: 0.6791 (m-80) cc_final: 0.6242 (m-80) REVERT: C 615 SER cc_start: 0.8133 (m) cc_final: 0.7434 (t) REVERT: C 623 ASP cc_start: 0.7028 (t0) cc_final: 0.6331 (t0) REVERT: C 646 ASN cc_start: 0.7157 (t0) cc_final: 0.6793 (t0) REVERT: C 647 LEU cc_start: 0.7432 (mt) cc_final: 0.6983 (mp) REVERT: C 652 ASN cc_start: 0.7383 (p0) cc_final: 0.6859 (p0) REVERT: C 669 ILE cc_start: 0.8447 (mm) cc_final: 0.8154 (mm) REVERT: C 821 ASN cc_start: 0.7251 (m-40) cc_final: 0.6912 (m110) REVERT: C 822 TYR cc_start: 0.6705 (m-80) cc_final: 0.5725 (m-80) REVERT: C 857 VAL cc_start: 0.7919 (t) cc_final: 0.7475 (m) REVERT: C 922 TYR cc_start: 0.7865 (m-80) cc_final: 0.7420 (m-80) REVERT: C 977 VAL cc_start: 0.7255 (t) cc_final: 0.6430 (m) REVERT: C 994 MET cc_start: 0.7075 (tpp) cc_final: 0.6407 (tpp) REVERT: C 1026 LEU cc_start: 0.1726 (OUTLIER) cc_final: 0.0385 (tp) REVERT: C 1036 ASN cc_start: 0.7847 (m-40) cc_final: 0.7244 (t0) REVERT: C 1060 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6823 (tt0) REVERT: C 1071 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7514 (mm110) REVERT: C 1094 SER cc_start: 0.8003 (m) cc_final: 0.7395 (t) REVERT: C 1191 TYR cc_start: 0.5846 (t80) cc_final: 0.5111 (t80) REVERT: B 56 TYR cc_start: 0.7656 (m-80) cc_final: 0.7008 (m-80) REVERT: B 155 MET cc_start: 0.5115 (mmm) cc_final: 0.4401 (mmm) REVERT: B 264 ARG cc_start: 0.6812 (ptp-170) cc_final: 0.6339 (ptp90) REVERT: B 635 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6448 (tm-30) REVERT: B 674 SER cc_start: 0.7939 (t) cc_final: 0.7614 (p) REVERT: B 806 SER cc_start: 0.7571 (t) cc_final: 0.7278 (m) REVERT: B 820 SER cc_start: 0.7777 (t) cc_final: 0.7572 (m) REVERT: B 944 LYS cc_start: 0.7583 (ttmm) cc_final: 0.7237 (mmmm) REVERT: B 1015 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7058 (tt) REVERT: B 1059 GLN cc_start: 0.7333 (tp-100) cc_final: 0.7061 (tp40) REVERT: B 1073 GLN cc_start: 0.7405 (mt0) cc_final: 0.7123 (mt0) REVERT: B 1077 LEU cc_start: 0.8862 (mt) cc_final: 0.8551 (mp) REVERT: B 1195 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6153 (mm-30) REVERT: B 1214 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6613 (tmtm) outliers start: 85 outliers final: 64 residues processed: 480 average time/residue: 0.1652 time to fit residues: 128.3523 Evaluate side-chains 495 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 420 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain B residue 89 TRP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 15 optimal weight: 0.4980 chunk 224 optimal weight: 6.9990 chunk 309 optimal weight: 0.1980 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 0.0370 chunk 184 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 232 optimal weight: 0.0970 chunk 281 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.234120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.194534 restraints weight = 65025.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.199699 restraints weight = 34625.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.203151 restraints weight = 21767.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.205338 restraints weight = 15478.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.206345 restraints weight = 12149.936| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28478 Z= 0.102 Angle : 0.566 13.512 38867 Z= 0.287 Chirality : 0.043 0.259 4389 Planarity : 0.004 0.074 4991 Dihedral : 4.735 58.355 4001 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.65 % Allowed : 16.04 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.14), residues: 3545 helix: 1.26 (0.20), residues: 747 sheet: -0.10 (0.21), residues: 647 loop : -1.99 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 34 TYR 0.020 0.001 TYR B1148 PHE 0.024 0.001 PHE B 368 TRP 0.047 0.001 TRP B 89 HIS 0.004 0.001 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00230 (28405) covalent geometry : angle 0.56319 (38715) SS BOND : bond 0.00209 ( 67) SS BOND : angle 0.90320 ( 134) hydrogen bonds : bond 0.03411 ( 948) hydrogen bonds : angle 4.65838 ( 2757) link_NAG-ASN : bond 0.00387 ( 6) link_NAG-ASN : angle 1.82229 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 423 time to evaluate : 1.151 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: symmetry clash 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: symmetry clash REVERT: A 105 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7180 (ttpt) REVERT: A 186 LYS cc_start: 0.5022 (mmmm) cc_final: 0.4802 (mmmm) REVERT: A 213 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5589 (t80) REVERT: A 218 MET cc_start: 0.6722 (ttm) cc_final: 0.6341 (ttm) REVERT: A 236 TYR cc_start: 0.6889 (t80) cc_final: 0.6429 (t80) REVERT: A 237 VAL cc_start: 0.6200 (t) cc_final: 0.5803 (t) REVERT: A 271 ASP cc_start: 0.7269 (p0) cc_final: 0.6912 (p0) REVERT: A 287 LEU cc_start: 0.8047 (tp) cc_final: 0.7657 (tt) REVERT: A 387 THR cc_start: 0.3102 (OUTLIER) cc_final: 0.2569 (p) REVERT: A 624 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5390 (pp) REVERT: A 683 GLN cc_start: 0.6100 (tm-30) cc_final: 0.5755 (tm-30) REVERT: A 702 ASN cc_start: 0.7358 (t0) cc_final: 0.6985 (t0) REVERT: A 746 TYR cc_start: 0.6559 (t80) cc_final: 0.6067 (t80) REVERT: A 780 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4883 (mp0) REVERT: A 794 PHE cc_start: 0.6653 (p90) cc_final: 0.6251 (p90) REVERT: A 795 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7839 (t) REVERT: A 880 ASP cc_start: 0.2470 (OUTLIER) cc_final: 0.1366 (t0) REVERT: A 910 LYS cc_start: 0.4576 (mtpt) cc_final: 0.3935 (tttt) REVERT: A 916 VAL cc_start: 0.2770 (OUTLIER) cc_final: 0.2458 (p) REVERT: A 920 GLU cc_start: 0.7424 (pp20) cc_final: 0.7018 (pp20) REVERT: A 922 TYR cc_start: 0.7520 (m-80) cc_final: 0.7156 (m-80) REVERT: A 943 ILE cc_start: 0.7401 (mt) cc_final: 0.7002 (mt) REVERT: A 994 MET cc_start: 0.5236 (tpt) cc_final: 0.4844 (tpt) REVERT: A 1033 VAL cc_start: 0.8309 (m) cc_final: 0.8082 (p) REVERT: A 1036 ASN cc_start: 0.7791 (t0) cc_final: 0.7428 (t0) REVERT: A 1042 SER cc_start: 0.7572 (m) cc_final: 0.7232 (p) REVERT: A 1076 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7495 (ttp-170) REVERT: A 1115 LYS cc_start: 0.5489 (OUTLIER) cc_final: 0.4450 (mttm) REVERT: C 155 MET cc_start: 0.3139 (mmm) cc_final: 0.2582 (mmm) REVERT: C 203 TYR cc_start: 0.6184 (p90) cc_final: 0.5812 (p90) REVERT: C 266 TYR cc_start: 0.6834 (m-80) cc_final: 0.6526 (m-80) REVERT: C 615 SER cc_start: 0.8089 (m) cc_final: 0.7401 (t) REVERT: C 623 ASP cc_start: 0.6823 (t0) cc_final: 0.6181 (t0) REVERT: C 647 LEU cc_start: 0.7388 (mt) cc_final: 0.7012 (mp) REVERT: C 652 ASN cc_start: 0.7293 (p0) cc_final: 0.6955 (p0) REVERT: C 821 ASN cc_start: 0.7209 (m-40) cc_final: 0.6875 (m110) REVERT: C 822 TYR cc_start: 0.6714 (m-80) cc_final: 0.5775 (m-80) REVERT: C 857 VAL cc_start: 0.7910 (t) cc_final: 0.7473 (m) REVERT: C 922 TYR cc_start: 0.7834 (m-80) cc_final: 0.7390 (m-80) REVERT: C 977 VAL cc_start: 0.7210 (t) cc_final: 0.6334 (m) REVERT: C 994 MET cc_start: 0.7018 (tpp) cc_final: 0.6338 (tpp) REVERT: C 1026 LEU cc_start: 0.1793 (OUTLIER) cc_final: 0.0393 (tp) REVERT: C 1036 ASN cc_start: 0.7776 (m-40) cc_final: 0.7227 (t0) REVERT: C 1060 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6764 (tt0) REVERT: C 1094 SER cc_start: 0.7885 (m) cc_final: 0.7302 (t) REVERT: C 1109 LYS cc_start: 0.3814 (OUTLIER) cc_final: 0.2708 (ttmt) REVERT: C 1191 TYR cc_start: 0.5806 (t80) cc_final: 0.5169 (t80) REVERT: B 56 TYR cc_start: 0.7614 (m-80) cc_final: 0.6987 (m-80) REVERT: B 155 MET cc_start: 0.4411 (mmm) cc_final: 0.4016 (mmm) REVERT: B 635 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6438 (tm-30) REVERT: B 674 SER cc_start: 0.7784 (t) cc_final: 0.7473 (p) REVERT: B 943 ILE cc_start: 0.8088 (mm) cc_final: 0.7843 (mm) REVERT: B 944 LYS cc_start: 0.7358 (ttmm) cc_final: 0.7123 (mmmm) REVERT: B 1015 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7064 (tt) REVERT: B 1059 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6948 (tp-100) REVERT: B 1073 GLN cc_start: 0.7289 (mt0) cc_final: 0.7052 (mt0) REVERT: B 1077 LEU cc_start: 0.8852 (mt) cc_final: 0.8553 (mp) REVERT: B 1195 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6001 (mm-30) REVERT: B 1214 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6503 (tmtm) outliers start: 83 outliers final: 62 residues processed: 479 average time/residue: 0.1807 time to fit residues: 139.8703 Evaluate side-chains 491 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 417 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1044 LEU Chi-restraints excluded: chain C residue 1109 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain B residue 89 TRP Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1126 ASN Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 136 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 337 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.230406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.188875 restraints weight = 63761.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.195383 restraints weight = 35594.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.197395 restraints weight = 22988.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.201415 restraints weight = 15864.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.200742 restraints weight = 12405.774| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28478 Z= 0.171 Angle : 0.629 14.663 38867 Z= 0.324 Chirality : 0.045 0.313 4389 Planarity : 0.004 0.065 4991 Dihedral : 5.039 56.382 4000 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.72 % Allowed : 16.17 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.14), residues: 3545 helix: 1.01 (0.20), residues: 738 sheet: -0.31 (0.20), residues: 661 loop : -2.01 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 34 TYR 0.022 0.001 TYR B 203 PHE 0.026 0.002 PHE C1143 TRP 0.041 0.002 TRP B 89 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00371 (28405) covalent geometry : angle 0.62310 (38715) SS BOND : bond 0.00422 ( 67) SS BOND : angle 1.37674 ( 134) hydrogen bonds : bond 0.04194 ( 948) hydrogen bonds : angle 4.97639 ( 2757) link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 2.01193 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6190.47 seconds wall clock time: 107 minutes 24.50 seconds (6444.50 seconds total)