Starting phenix.real_space_refine on Mon May 26 06:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8i_39047/05_2025/8y8i_39047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8i_39047/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8i_39047/05_2025/8y8i_39047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8i_39047/05_2025/8y8i_39047.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8i_39047/05_2025/8y8i_39047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8i_39047/05_2025/8y8i_39047.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} 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: 15.86, per 1000 atoms: 0.57 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: 6.54 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 4.39 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: 13.74 Time building geometry restraints manager: 7.71 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 1221 or resid 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 1221 \ or resid 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 1221 or resid 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: 2.570 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: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 64.160 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 344 HIS 0.002 0.000 HIS C 201 PHE 0.007 0.001 PHE A 764 TYR 0.009 0.001 TYR A1148 ARG 0.001 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.02929 ( 18) hydrogen bonds : bond 0.14389 ( 948) hydrogen bonds : angle 5.93161 ( 2757) SS BOND : bond 0.00106 ( 67) SS BOND : angle 0.44077 ( 134) covalent geometry : bond 0.00161 (28405) covalent geometry : angle 0.39531 (38715) *********************** 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 : 3.123 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 52 LEU cc_start: 0.6969 (mp) cc_final: 0.6597 (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: 0.7423 (p0) REVERT: A 155 MET cc_start: 0.3566 (mmm) cc_final: 0.3174 (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: 0.6214 (t80) REVERT: A 287 LEU cc_start: 0.7732 (tp) cc_final: 0.6977 (tp) REVERT: A 387 THR cc_start: 0.2791 (OUTLIER) cc_final: 0.2181 (p) REVERT: A 623 ASP cc_start: 0.6415 (t0) cc_final: 0.5951 (t0) REVERT: A 648 LEU cc_start: 0.7258 (tp) cc_final: 0.6053 (tp) REVERT: A 922 TYR cc_start: 0.7417 (m-80) cc_final: 0.7140 (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: 0.5433 (mt) REVERT: A 1036 ASN cc_start: 0.7748 (t0) cc_final: 0.7436 (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: 0.7923 (m110) REVERT: A 1081 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7356 (ttm170) REVERT: A 1100 LYS cc_start: 0.6756 (mmmm) cc_final: 0.6551 (tppt) REVERT: A 1115 LYS cc_start: 0.4605 (OUTLIER) cc_final: 0.4204 (ttmm) REVERT: C 215 ASP cc_start: 0.4671 (p0) cc_final: 0.3084 (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: 0.5772 (m-80) REVERT: C 615 SER cc_start: 0.7616 (m) cc_final: 0.7294 (t) REVERT: C 623 ASP cc_start: 0.6686 (t0) cc_final: 0.6480 (t70) REVERT: C 634 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6025 (mttp) REVERT: C 656 ILE cc_start: 0.6345 (pt) cc_final: 0.5966 (mt) REVERT: C 734 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6623 (m) REVERT: C 812 ILE cc_start: 0.8468 (mt) cc_final: 0.8216 (mm) REVERT: C 821 ASN cc_start: 0.7051 (m-40) cc_final: 0.6730 (m-40) REVERT: C 822 TYR cc_start: 0.6064 (m-80) cc_final: 0.5756 (m-80) REVERT: C 857 VAL cc_start: 0.7790 (t) cc_final: 0.7358 (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: 0.6621 (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: 0.7199 (t0) REVERT: C 1075 ASP cc_start: 0.6717 (m-30) cc_final: 0.5879 (m-30) REVERT: C 1094 SER cc_start: 0.7415 (m) cc_final: 0.6839 (t) REVERT: C 1096 ILE cc_start: 0.8239 (tp) cc_final: 0.7954 (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: 0.3945 (t80) REVERT: B 266 TYR cc_start: 0.7661 (m-80) cc_final: 0.7024 (m-80) REVERT: B 289 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7054 (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: 0.7421 (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: 0.7051 (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: 0.6522 (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: 0.3343 (m) REVERT: B 1214 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6787 (tmtm) outliers start: 97 outliers final: 34 residues processed: 643 average time/residue: 0.3684 time to fit residues: 378.8209 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 : 2.713 ------------------------------------------------------------------------------- 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 299 optimal weight: 0.3980 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 169 optimal weight: 0.0370 chunk 207 optimal weight: 0.4980 chunk 322 optimal weight: 8.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 881 ASN ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN A1059 GLN A1201 ASN C 19 ASN C 248 ASN C 291 GLN C 410 GLN C 595 ASN 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 909 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.237383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.200109 restraints weight = 65651.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.206397 restraints weight = 34976.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.208948 restraints weight = 21968.322| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28478 Z= 0.114 Angle : 0.540 14.159 38867 Z= 0.274 Chirality : 0.044 0.689 4389 Planarity : 0.004 0.053 4991 Dihedral : 4.965 59.571 4044 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.75 % Allowed : 9.33 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3545 helix: 0.93 (0.19), residues: 734 sheet: -0.72 (0.19), residues: 659 loop : -2.48 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 174 HIS 0.008 0.001 HIS C 160 PHE 0.025 0.001 PHE C 473 TYR 0.033 0.001 TYR B1193 ARG 0.003 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.01856 ( 6) link_NAG-ASN : angle 3.51135 ( 18) hydrogen bonds : bond 0.03474 ( 948) hydrogen bonds : angle 4.68549 ( 2757) SS BOND : bond 0.00355 ( 67) SS BOND : angle 1.05808 ( 134) covalent geometry : bond 0.00246 (28405) covalent geometry : angle 0.53181 (38715) *********************** 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 563 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 477 time to evaluate : 2.900 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: A 120 GLU cc_start: 0.5201 (mp0) cc_final: 0.4919 (mm-30) REVERT: A 132 ASN cc_start: 0.7694 (p0) cc_final: 0.7468 (p0) REVERT: A 155 MET cc_start: 0.3830 (mmm) cc_final: 0.3369 (mmm) REVERT: A 218 MET cc_start: 0.6577 (ttm) cc_final: 0.6318 (ttm) REVERT: A 236 TYR cc_start: 0.6756 (t80) cc_final: 0.6157 (t80) REVERT: A 277 THR cc_start: 0.8574 (m) cc_final: 0.8229 (p) REVERT: A 287 LEU cc_start: 0.7891 (tp) cc_final: 0.7591 (tp) REVERT: A 387 THR cc_start: 0.2674 (OUTLIER) cc_final: 0.2108 (p) REVERT: A 623 ASP cc_start: 0.6241 (t0) cc_final: 0.5807 (t0) REVERT: A 624 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4828 (pp) REVERT: A 683 GLN cc_start: 0.5482 (tm-30) cc_final: 0.5256 (tm-30) REVERT: A 702 ASN cc_start: 0.7381 (t0) cc_final: 0.7035 (t0) REVERT: A 712 TYR cc_start: 0.4982 (p90) cc_final: 0.4726 (p90) REVERT: A 780 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.5146 (mp0) REVERT: A 794 PHE cc_start: 0.6598 (p90) cc_final: 0.6167 (p90) REVERT: A 795 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7286 (t) REVERT: A 923 ASN cc_start: 0.6663 (t0) cc_final: 0.6254 (m110) REVERT: A 994 MET cc_start: 0.5334 (tpt) cc_final: 0.4547 (tpt) REVERT: A 1036 ASN cc_start: 0.7795 (t0) cc_final: 0.7556 (t0) REVERT: A 1042 SER cc_start: 0.7306 (m) cc_final: 0.6967 (p) REVERT: A 1055 SER cc_start: 0.8583 (p) cc_final: 0.8259 (m) REVERT: A 1061 ILE cc_start: 0.8571 (mt) cc_final: 0.8365 (mt) REVERT: A 1115 LYS cc_start: 0.4685 (OUTLIER) cc_final: 0.3734 (mttp) REVERT: A 1205 MET cc_start: 0.6297 (ttp) cc_final: 0.6087 (ttp) REVERT: C 155 MET cc_start: 0.4350 (mmm) cc_final: 0.3456 (mmm) REVERT: C 174 TRP cc_start: 0.6664 (p-90) cc_final: 0.6275 (p-90) REVERT: C 615 SER cc_start: 0.8056 (m) cc_final: 0.7375 (t) REVERT: C 623 ASP cc_start: 0.7103 (t0) cc_final: 0.6551 (t0) REVERT: C 624 LEU cc_start: 0.7537 (pp) cc_final: 0.7236 (pt) REVERT: C 632 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7301 (mp) REVERT: C 634 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5899 (tttt) REVERT: C 821 ASN cc_start: 0.7120 (m-40) cc_final: 0.6819 (m-40) REVERT: C 822 TYR cc_start: 0.6098 (m-80) cc_final: 0.5755 (m-80) REVERT: C 840 ASN cc_start: 0.7935 (m110) cc_final: 0.7694 (m-40) REVERT: C 843 LEU cc_start: 0.8720 (mt) cc_final: 0.8414 (mp) REVERT: C 977 VAL cc_start: 0.7020 (t) cc_final: 0.6093 (m) REVERT: C 994 MET cc_start: 0.6783 (tpp) cc_final: 0.6051 (tpp) REVERT: C 1036 ASN cc_start: 0.7820 (m-40) cc_final: 0.7225 (t0) REVERT: C 1043 LEU cc_start: 0.7904 (pp) cc_final: 0.7647 (tp) REVERT: C 1071 GLN cc_start: 0.7487 (mm110) cc_final: 0.6416 (mm110) REVERT: C 1075 ASP cc_start: 0.7081 (m-30) cc_final: 0.6597 (m-30) REVERT: C 1094 SER cc_start: 0.7631 (m) cc_final: 0.7036 (t) REVERT: C 1096 ILE cc_start: 0.8289 (tp) cc_final: 0.8053 (tp) REVERT: C 1129 HIS cc_start: 0.5492 (t-90) cc_final: 0.5268 (t-90) REVERT: B 155 MET cc_start: 0.5326 (mmm) cc_final: 0.4576 (mmm) REVERT: B 209 PHE cc_start: 0.6828 (t80) cc_final: 0.3837 (t80) REVERT: B 257 TRP cc_start: 0.6817 (m100) cc_final: 0.6065 (m100) REVERT: B 273 HIS cc_start: 0.7418 (m-70) cc_final: 0.7093 (m90) REVERT: B 293 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7784 (ttmm) REVERT: B 731 VAL cc_start: 0.7123 (p) cc_final: 0.6781 (t) REVERT: B 813 ASP cc_start: 0.6624 (p0) cc_final: 0.5899 (p0) REVERT: B 949 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7093 (tp) REVERT: B 1059 GLN cc_start: 0.7268 (tp40) cc_final: 0.6920 (tp-100) REVERT: B 1060 GLU cc_start: 0.7068 (tt0) cc_final: 0.6387 (tt0) REVERT: B 1062 LEU cc_start: 0.8390 (mm) cc_final: 0.8155 (mt) REVERT: B 1064 ARG cc_start: 0.6986 (mtm110) cc_final: 0.6568 (mtm110) REVERT: B 1073 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7024 (mp10) REVERT: B 1099 ILE cc_start: 0.8193 (tt) cc_final: 0.7857 (pt) REVERT: B 1205 MET cc_start: 0.3139 (mpp) cc_final: 0.2757 (mpp) REVERT: B 1214 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6733 (tmtm) outliers start: 86 outliers final: 51 residues processed: 534 average time/residue: 0.3686 time to fit residues: 316.6975 Evaluate side-chains 491 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 431 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 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 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 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 96 SER Chi-restraints excluded: chain C residue 193 VAL 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 677 VAL 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 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 630 GLN Chi-restraints excluded: chain B residue 650 ASP 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 815 SER 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 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 1020 THR 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 135 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 53 ASN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN A1221 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN B 142 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 821 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.232795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.192347 restraints weight = 63928.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.198543 restraints weight = 35780.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.202432 restraints weight = 20275.665| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28478 Z= 0.161 Angle : 0.553 15.262 38867 Z= 0.287 Chirality : 0.044 0.353 4389 Planarity : 0.004 0.057 4991 Dihedral : 4.914 59.805 4027 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.39 % Allowed : 10.77 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3545 helix: 0.83 (0.19), residues: 755 sheet: -0.57 (0.19), residues: 660 loop : -2.40 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 971 HIS 0.003 0.001 HIS B 826 PHE 0.019 0.002 PHE C1143 TYR 0.027 0.002 TYR B 203 ARG 0.007 0.000 ARG B 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 6) link_NAG-ASN : angle 2.00260 ( 18) hydrogen bonds : bond 0.04072 ( 948) hydrogen bonds : angle 4.81894 ( 2757) SS BOND : bond 0.00501 ( 67) SS BOND : angle 1.02451 ( 134) covalent geometry : bond 0.00342 (28405) covalent geometry : angle 0.54950 (38715) *********************** 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 566 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 460 time to evaluate : 2.840 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 96 SER cc_start: 0.7987 (t) cc_final: 0.7762 (t) REVERT: A 120 GLU cc_start: 0.5649 (mp0) cc_final: 0.5154 (mp0) REVERT: A 132 ASN cc_start: 0.7802 (p0) cc_final: 0.7588 (p0) REVERT: A 186 LYS cc_start: 0.5145 (mmmm) cc_final: 0.4893 (mmmm) REVERT: A 213 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.5834 (t80) REVERT: A 218 MET cc_start: 0.6673 (ttm) cc_final: 0.6310 (ttm) REVERT: A 236 TYR cc_start: 0.6816 (t80) cc_final: 0.6216 (t80) REVERT: A 258 VAL cc_start: 0.7803 (t) cc_final: 0.7588 (t) REVERT: A 287 LEU cc_start: 0.8053 (tp) cc_final: 0.7481 (tp) REVERT: A 387 THR cc_start: 0.2870 (OUTLIER) cc_final: 0.2335 (p) REVERT: A 623 ASP cc_start: 0.6078 (t0) cc_final: 0.5699 (t0) REVERT: A 624 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4980 (pp) REVERT: A 646 ASN cc_start: 0.5471 (m-40) cc_final: 0.4716 (m-40) REVERT: A 683 GLN cc_start: 0.5733 (tm-30) cc_final: 0.5459 (tm-30) REVERT: A 702 ASN cc_start: 0.7472 (t0) cc_final: 0.7127 (t0) REVERT: A 762 TYR cc_start: 0.6073 (m-10) cc_final: 0.5777 (m-10) REVERT: A 780 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5273 (mp0) REVERT: A 794 PHE cc_start: 0.6834 (p90) cc_final: 0.6421 (p90) REVERT: A 795 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7767 (t) REVERT: A 822 TYR cc_start: 0.6930 (m-80) cc_final: 0.6636 (m-80) REVERT: A 827 ASP cc_start: 0.7047 (m-30) cc_final: 0.6838 (m-30) REVERT: A 880 ASP cc_start: 0.2481 (OUTLIER) cc_final: 0.1529 (t0) REVERT: A 922 TYR cc_start: 0.7728 (m-80) cc_final: 0.7381 (m-80) REVERT: A 994 MET cc_start: 0.5587 (tpt) cc_final: 0.4847 (tpt) REVERT: A 1036 ASN cc_start: 0.7884 (t0) cc_final: 0.7642 (t0) REVERT: A 1042 SER cc_start: 0.7569 (m) cc_final: 0.7211 (p) REVERT: A 1055 SER cc_start: 0.8575 (p) cc_final: 0.8249 (m) REVERT: A 1061 ILE cc_start: 0.8831 (mt) cc_final: 0.8568 (mt) REVERT: A 1205 MET cc_start: 0.6875 (ttp) cc_final: 0.6548 (ttp) REVERT: C 155 MET cc_start: 0.4918 (mmm) cc_final: 0.3922 (mmm) REVERT: C 615 SER cc_start: 0.8063 (m) cc_final: 0.7333 (t) REVERT: C 623 ASP cc_start: 0.7134 (t0) cc_final: 0.6577 (t0) REVERT: C 634 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.6081 (ttmt) REVERT: C 643 ASN cc_start: 0.7760 (m-40) cc_final: 0.7541 (m-40) REVERT: C 647 LEU cc_start: 0.7705 (mt) cc_final: 0.7369 (mp) REVERT: C 730 SER cc_start: 0.6862 (OUTLIER) cc_final: 0.6662 (t) REVERT: C 821 ASN cc_start: 0.7263 (m-40) cc_final: 0.6952 (m-40) REVERT: C 822 TYR cc_start: 0.6284 (m-80) cc_final: 0.5769 (m-80) REVERT: C 977 VAL cc_start: 0.7239 (t) cc_final: 0.6344 (m) REVERT: C 994 MET cc_start: 0.6975 (tpp) cc_final: 0.6171 (tpp) REVERT: C 1036 ASN cc_start: 0.7845 (m-40) cc_final: 0.7280 (t0) REVERT: C 1041 ASN cc_start: 0.7540 (m-40) cc_final: 0.7271 (m-40) REVERT: C 1043 LEU cc_start: 0.8037 (pp) cc_final: 0.7699 (tp) REVERT: C 1060 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6954 (tt0) REVERT: C 1071 GLN cc_start: 0.7725 (mm110) cc_final: 0.7398 (mm110) REVERT: C 1094 SER cc_start: 0.7916 (m) cc_final: 0.7264 (t) REVERT: C 1096 ILE cc_start: 0.8377 (tp) cc_final: 0.8076 (tp) REVERT: B 56 TYR cc_start: 0.7570 (m-80) cc_final: 0.6792 (m-80) REVERT: B 155 MET cc_start: 0.5854 (mmm) cc_final: 0.3887 (mmm) REVERT: B 157 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7686 (tp30) REVERT: B 635 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6633 (tm-30) REVERT: B 666 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 708 SER cc_start: 0.7516 (p) cc_final: 0.7197 (t) REVERT: B 731 VAL cc_start: 0.7345 (p) cc_final: 0.7040 (t) REVERT: B 949 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7180 (tp) REVERT: B 955 ILE cc_start: 0.5499 (mt) cc_final: 0.5028 (mt) REVERT: B 1059 GLN cc_start: 0.7342 (tp-100) cc_final: 0.6961 (tp-100) REVERT: B 1064 ARG cc_start: 0.6897 (mtm110) cc_final: 0.6512 (mtm110) REVERT: B 1073 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6948 (mp10) REVERT: B 1096 ILE cc_start: 0.7977 (mm) cc_final: 0.7705 (tp) REVERT: B 1099 ILE cc_start: 0.8254 (tt) cc_final: 0.7960 (pt) REVERT: B 1195 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5798 (mm-30) REVERT: B 1214 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6705 (tmtm) outliers start: 106 outliers final: 66 residues processed: 522 average time/residue: 0.3863 time to fit residues: 324.8850 Evaluate side-chains 511 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 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 880 ASP 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 A residue 1158 VAL 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 329 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 652 ASN 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 730 SER Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 951 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1170 ILE 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 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 666 THR 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 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 887 LEU 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 949 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1002 LYS 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 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 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 320 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 305 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 337 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 847 ASN ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 ASN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN B 821 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.234518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.194249 restraints weight = 64572.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.201028 restraints weight = 35455.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.202984 restraints weight = 20257.113| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28478 Z= 0.119 Angle : 0.521 14.714 38867 Z= 0.269 Chirality : 0.043 0.276 4389 Planarity : 0.004 0.057 4991 Dihedral : 4.860 57.468 4025 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.67 % Allowed : 11.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3545 helix: 1.08 (0.20), residues: 753 sheet: -0.51 (0.20), residues: 650 loop : -2.27 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 444 HIS 0.007 0.001 HIS B 142 PHE 0.025 0.001 PHE C 67 TYR 0.018 0.001 TYR B 641 ARG 0.006 0.000 ARG B 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 6) link_NAG-ASN : angle 1.80034 ( 18) hydrogen bonds : bond 0.03554 ( 948) hydrogen bonds : angle 4.65159 ( 2757) SS BOND : bond 0.00284 ( 67) SS BOND : angle 1.22099 ( 134) covalent geometry : bond 0.00261 (28405) covalent geometry : angle 0.51520 (38715) *********************** 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 558 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 443 time to evaluate : 2.978 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: A 96 SER cc_start: 0.8019 (t) cc_final: 0.7814 (t) REVERT: A 105 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7159 (ttpt) REVERT: A 132 ASN cc_start: 0.7821 (p0) cc_final: 0.7594 (p0) REVERT: A 186 LYS cc_start: 0.5192 (mmmm) cc_final: 0.4983 (mmmm) REVERT: A 213 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5752 (t80) REVERT: A 236 TYR cc_start: 0.6798 (t80) cc_final: 0.6245 (t80) REVERT: A 286 PHE cc_start: 0.7678 (m-80) cc_final: 0.6449 (m-10) REVERT: A 287 LEU cc_start: 0.8013 (tp) cc_final: 0.7721 (tp) REVERT: A 387 THR cc_start: 0.2881 (OUTLIER) cc_final: 0.2293 (p) REVERT: A 623 ASP cc_start: 0.6097 (t0) cc_final: 0.5778 (t0) REVERT: A 624 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.5070 (pp) REVERT: A 646 ASN cc_start: 0.5188 (OUTLIER) cc_final: 0.4248 (m-40) REVERT: A 683 GLN cc_start: 0.5858 (tm-30) cc_final: 0.5578 (tm-30) REVERT: A 702 ASN cc_start: 0.7532 (t0) cc_final: 0.7182 (t0) REVERT: A 762 TYR cc_start: 0.6126 (m-10) cc_final: 0.5852 (m-10) REVERT: A 780 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: A 794 PHE cc_start: 0.6675 (p90) cc_final: 0.6231 (p90) REVERT: A 795 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 827 ASP cc_start: 0.6947 (m-30) cc_final: 0.6725 (m-30) REVERT: A 910 LYS cc_start: 0.4157 (mtpt) cc_final: 0.3379 (ttpp) REVERT: A 994 MET cc_start: 0.5532 (tpt) cc_final: 0.5110 (tpt) REVERT: A 1036 ASN cc_start: 0.7779 (t0) cc_final: 0.7522 (t0) REVERT: A 1042 SER cc_start: 0.7419 (m) cc_final: 0.7063 (p) REVERT: A 1055 SER cc_start: 0.8425 (p) cc_final: 0.8219 (m) REVERT: A 1061 ILE cc_start: 0.8780 (mt) cc_final: 0.8539 (mt) REVERT: A 1205 MET cc_start: 0.6877 (ttp) cc_final: 0.6582 (ttp) REVERT: C 155 MET cc_start: 0.4719 (mmm) cc_final: 0.3930 (mmm) REVERT: C 281 ASP cc_start: 0.6401 (m-30) cc_final: 0.6165 (t70) REVERT: C 291 GLN cc_start: 0.7105 (mt0) cc_final: 0.6572 (mt0) REVERT: C 312 LYS cc_start: 0.7414 (tptt) cc_final: 0.7187 (tptt) REVERT: C 615 SER cc_start: 0.8007 (m) cc_final: 0.7301 (t) REVERT: C 623 ASP cc_start: 0.6997 (t0) cc_final: 0.6454 (t0) REVERT: C 634 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5867 (tttt) REVERT: C 646 ASN cc_start: 0.7297 (t0) cc_final: 0.7018 (t0) REVERT: C 647 LEU cc_start: 0.7461 (mt) cc_final: 0.7070 (mp) REVERT: C 651 SER cc_start: 0.8917 (m) cc_final: 0.8626 (p) REVERT: C 730 SER cc_start: 0.6822 (p) cc_final: 0.6622 (t) REVERT: C 821 ASN cc_start: 0.7215 (m-40) cc_final: 0.6939 (m-40) REVERT: C 822 TYR cc_start: 0.6367 (m-80) cc_final: 0.5742 (m-80) REVERT: C 828 LEU cc_start: 0.8111 (tp) cc_final: 0.7591 (tt) REVERT: C 922 TYR cc_start: 0.7754 (m-10) cc_final: 0.7471 (m-10) REVERT: C 977 VAL cc_start: 0.7307 (t) cc_final: 0.6421 (m) REVERT: C 994 MET cc_start: 0.6919 (tpp) cc_final: 0.6172 (tpp) REVERT: C 1036 ASN cc_start: 0.7878 (m-40) cc_final: 0.7286 (t0) REVERT: C 1043 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7609 (tp) REVERT: C 1060 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6905 (tt0) REVERT: C 1071 GLN cc_start: 0.7775 (mm110) cc_final: 0.7122 (mm110) REVERT: C 1075 ASP cc_start: 0.7345 (m-30) cc_final: 0.6910 (m-30) REVERT: C 1094 SER cc_start: 0.7782 (m) cc_final: 0.7188 (t) REVERT: C 1096 ILE cc_start: 0.8334 (tp) cc_final: 0.8067 (tp) REVERT: B 56 TYR cc_start: 0.7558 (m-80) cc_final: 0.6730 (m-80) REVERT: B 264 ARG cc_start: 0.6765 (ptp-170) cc_final: 0.6393 (ptp90) REVERT: B 635 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6594 (tm-30) REVERT: B 674 SER cc_start: 0.7866 (t) cc_final: 0.7628 (p) REVERT: B 708 SER cc_start: 0.7507 (p) cc_final: 0.7184 (t) REVERT: B 731 VAL cc_start: 0.7327 (p) cc_final: 0.7063 (t) REVERT: B 955 ILE cc_start: 0.5416 (mt) cc_final: 0.4980 (mt) REVERT: B 967 MET cc_start: 0.3707 (tpp) cc_final: 0.3481 (tpp) REVERT: B 1043 LEU cc_start: 0.8254 (tp) cc_final: 0.7846 (tt) REVERT: B 1059 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6824 (tp-100) REVERT: B 1073 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6875 (mp10) REVERT: B 1096 ILE cc_start: 0.8010 (mm) cc_final: 0.7727 (tp) REVERT: B 1195 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6066 (mm-30) REVERT: B 1205 MET cc_start: 0.3191 (mpp) cc_final: 0.2758 (mpp) REVERT: B 1214 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6880 (tmtm) outliers start: 115 outliers final: 71 residues processed: 513 average time/residue: 0.3645 time to fit residues: 303.7530 Evaluate side-chains 505 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 425 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 190 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 646 ASN 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 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 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 317 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 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 744 ILE Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1043 LEU 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 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 131 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 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 814 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 887 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 909 ASN 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 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 30 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 297 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 0.0370 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- 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 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 ASN ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1079 ASN B 703 ASN 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 = 0.4848 r_free = 0.4848 target = 0.231833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.190725 restraints weight = 63308.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.196644 restraints weight = 36083.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201275 restraints weight = 19973.707| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.3183 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= 0.160 Angle : 0.550 14.886 38867 Z= 0.288 Chirality : 0.043 0.258 4389 Planarity : 0.004 0.055 4991 Dihedral : 4.951 57.866 4018 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.58 % Allowed : 12.62 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3545 helix: 0.93 (0.19), residues: 757 sheet: -0.46 (0.20), residues: 653 loop : -2.27 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 444 HIS 0.006 0.001 HIS C1129 PHE 0.026 0.001 PHE C1143 TYR 0.023 0.001 TYR B 203 ARG 0.005 0.000 ARG B 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 1.71090 ( 18) hydrogen bonds : bond 0.03976 ( 948) hydrogen bonds : angle 4.81513 ( 2757) SS BOND : bond 0.00310 ( 67) SS BOND : angle 1.25137 ( 134) covalent geometry : bond 0.00340 (28405) covalent geometry : angle 0.54451 (38715) *********************** 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 555 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 443 time to evaluate : 2.712 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 34 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7718 (ttp80) REVERT: A 96 SER cc_start: 0.8037 (t) cc_final: 0.7819 (t) REVERT: A 105 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7283 (ttpt) REVERT: A 186 LYS cc_start: 0.5475 (mmmm) cc_final: 0.5246 (mmmt) REVERT: A 213 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5907 (t80) REVERT: A 218 MET cc_start: 0.6655 (ttm) cc_final: 0.6284 (ttm) REVERT: A 236 TYR cc_start: 0.6928 (t80) cc_final: 0.6382 (t80) REVERT: A 287 LEU cc_start: 0.8146 (tp) cc_final: 0.7928 (tp) REVERT: A 387 THR cc_start: 0.2890 (OUTLIER) cc_final: 0.2334 (p) REVERT: A 623 ASP cc_start: 0.6052 (t0) cc_final: 0.5749 (t0) REVERT: A 624 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5290 (pp) REVERT: A 646 ASN cc_start: 0.5319 (OUTLIER) cc_final: 0.4949 (m110) REVERT: A 683 GLN cc_start: 0.5845 (tm-30) cc_final: 0.5567 (tm-30) REVERT: A 702 ASN cc_start: 0.7596 (t0) cc_final: 0.7287 (t0) REVERT: A 780 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5259 (mp0) REVERT: A 794 PHE cc_start: 0.6791 (p90) cc_final: 0.6377 (p90) REVERT: A 795 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7904 (t) REVERT: A 827 ASP cc_start: 0.6883 (m-30) cc_final: 0.6657 (m-30) REVERT: A 880 ASP cc_start: 0.2456 (OUTLIER) cc_final: 0.1463 (t0) REVERT: A 910 LYS cc_start: 0.4206 (mtpt) cc_final: 0.3369 (ttpp) REVERT: A 922 TYR cc_start: 0.7632 (m-80) cc_final: 0.7330 (m-80) REVERT: A 943 ILE cc_start: 0.7648 (mt) cc_final: 0.7269 (mt) REVERT: A 994 MET cc_start: 0.5526 (tpt) cc_final: 0.5090 (tpt) REVERT: A 1033 VAL cc_start: 0.8265 (m) cc_final: 0.8045 (p) REVERT: A 1036 ASN cc_start: 0.7798 (t0) cc_final: 0.7492 (t0) REVERT: A 1042 SER cc_start: 0.7516 (m) cc_final: 0.7145 (p) REVERT: A 1055 SER cc_start: 0.8481 (p) cc_final: 0.8218 (m) REVERT: A 1061 ILE cc_start: 0.8744 (mt) cc_final: 0.8530 (mt) REVERT: A 1076 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7808 (mtm-85) REVERT: A 1115 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.4530 (mmmt) REVERT: A 1120 ARG cc_start: 0.5701 (tpp80) cc_final: 0.4943 (mmt180) REVERT: A 1205 MET cc_start: 0.6944 (ttp) cc_final: 0.6645 (ttp) REVERT: C 155 MET cc_start: 0.4637 (mmm) cc_final: 0.4097 (mmm) REVERT: C 174 TRP cc_start: 0.6993 (p-90) cc_final: 0.6448 (p-90) REVERT: C 238 MET cc_start: 0.3463 (ptt) cc_final: 0.3044 (ptt) REVERT: C 615 SER cc_start: 0.8016 (m) cc_final: 0.7336 (t) REVERT: C 623 ASP cc_start: 0.7005 (t0) cc_final: 0.6527 (t0) REVERT: C 647 LEU cc_start: 0.7597 (mt) cc_final: 0.7223 (mp) REVERT: C 651 SER cc_start: 0.9072 (m) cc_final: 0.8803 (p) REVERT: C 821 ASN cc_start: 0.7275 (m-40) cc_final: 0.6974 (m-40) REVERT: C 822 TYR cc_start: 0.6515 (m-80) cc_final: 0.5834 (m-80) REVERT: C 828 LEU cc_start: 0.8145 (tp) cc_final: 0.7564 (tt) REVERT: C 922 TYR cc_start: 0.7824 (m-10) cc_final: 0.7473 (m-10) REVERT: C 977 VAL cc_start: 0.7324 (t) cc_final: 0.6456 (m) REVERT: C 994 MET cc_start: 0.7041 (tpp) cc_final: 0.6299 (tpp) REVERT: C 1041 ASN cc_start: 0.7392 (m-40) cc_final: 0.7184 (m-40) REVERT: C 1043 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7645 (tp) REVERT: C 1060 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6897 (tt0) REVERT: C 1071 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7362 (mm-40) REVERT: C 1075 ASP cc_start: 0.7510 (m-30) cc_final: 0.6874 (m-30) REVERT: C 1079 ASN cc_start: 0.8052 (m-40) cc_final: 0.7844 (m-40) REVERT: C 1094 SER cc_start: 0.7908 (m) cc_final: 0.7337 (t) REVERT: C 1096 ILE cc_start: 0.8391 (tp) cc_final: 0.8106 (tp) REVERT: B 56 TYR cc_start: 0.7589 (m-80) cc_final: 0.6869 (m-80) REVERT: B 60 THR cc_start: 0.7412 (p) cc_final: 0.7196 (p) REVERT: B 155 MET cc_start: 0.5485 (mmm) cc_final: 0.4750 (mmm) REVERT: B 264 ARG cc_start: 0.6852 (ptp-170) cc_final: 0.6470 (ptp90) REVERT: B 635 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6506 (tm-30) REVERT: B 674 SER cc_start: 0.7894 (t) cc_final: 0.7679 (p) REVERT: B 708 SER cc_start: 0.7539 (p) cc_final: 0.7247 (t) REVERT: B 731 VAL cc_start: 0.7281 (p) cc_final: 0.7022 (t) REVERT: B 806 SER cc_start: 0.7617 (t) cc_final: 0.7250 (m) REVERT: B 933 ASP cc_start: 0.6491 (t70) cc_final: 0.6262 (t70) REVERT: B 949 ILE cc_start: 0.7607 (pt) cc_final: 0.7193 (tp) REVERT: B 955 ILE cc_start: 0.5533 (mt) cc_final: 0.4940 (mt) REVERT: B 967 MET cc_start: 0.3931 (tpp) cc_final: 0.3652 (tpp) REVERT: B 1059 GLN cc_start: 0.7268 (tp-100) cc_final: 0.6875 (tp-100) REVERT: B 1073 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6933 (mp10) REVERT: B 1096 ILE cc_start: 0.8059 (mm) cc_final: 0.7774 (tp) REVERT: B 1195 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6121 (mm-30) REVERT: B 1214 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6685 (tmtm) outliers start: 112 outliers final: 73 residues processed: 515 average time/residue: 0.3661 time to fit residues: 304.3029 Evaluate side-chains 508 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 425 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 190 THR 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 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 799 HIS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 880 ASP 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 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 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 317 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 1019 PHE Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1043 LEU 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 44 LEU 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 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 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 909 ASN 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 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL 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 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 340 optimal weight: 2.9990 chunk 319 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 234 optimal weight: 20.0000 chunk 322 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 155 optimal weight: 0.0050 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 938 GLN A 982 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.231459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.190449 restraints weight = 63774.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.197186 restraints weight = 34763.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.199546 restraints weight = 19365.674| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28478 Z= 0.168 Angle : 0.575 15.669 38867 Z= 0.302 Chirality : 0.044 0.260 4389 Planarity : 0.004 0.054 4991 Dihedral : 5.147 59.385 4013 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.55 % Allowed : 13.23 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3545 helix: 0.88 (0.19), residues: 746 sheet: -0.54 (0.20), residues: 680 loop : -2.24 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 444 HIS 0.005 0.001 HIS B 826 PHE 0.033 0.002 PHE C1143 TYR 0.024 0.002 TYR B 203 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 1.72305 ( 18) hydrogen bonds : bond 0.04209 ( 948) hydrogen bonds : angle 4.97132 ( 2757) SS BOND : bond 0.00379 ( 67) SS BOND : angle 1.15271 ( 134) covalent geometry : bond 0.00358 (28405) covalent geometry : angle 0.57073 (38715) *********************** 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 546 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 435 time to evaluate : 3.227 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: A 96 SER cc_start: 0.8042 (t) cc_final: 0.7784 (t) REVERT: A 105 LYS cc_start: 0.7617 (ttpt) cc_final: 0.7202 (ttpt) REVERT: A 155 MET cc_start: 0.4152 (mmm) cc_final: 0.3640 (mmm) REVERT: A 186 LYS cc_start: 0.5677 (mmmm) cc_final: 0.5397 (mmmt) REVERT: A 213 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5879 (t80) REVERT: A 218 MET cc_start: 0.6789 (ttm) cc_final: 0.6430 (ttm) REVERT: A 236 TYR cc_start: 0.6909 (t80) cc_final: 0.6345 (t80) REVERT: A 287 LEU cc_start: 0.8182 (tp) cc_final: 0.7952 (tp) REVERT: A 387 THR cc_start: 0.3002 (OUTLIER) cc_final: 0.2476 (p) REVERT: A 623 ASP cc_start: 0.6068 (t0) cc_final: 0.5794 (t0) REVERT: A 624 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5304 (pp) REVERT: A 683 GLN cc_start: 0.5861 (tm-30) cc_final: 0.5576 (tm-30) REVERT: A 702 ASN cc_start: 0.7661 (t0) cc_final: 0.7336 (t0) REVERT: A 746 TYR cc_start: 0.6326 (t80) cc_final: 0.5817 (t80) REVERT: A 780 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5343 (mp0) REVERT: A 794 PHE cc_start: 0.6892 (p90) cc_final: 0.6483 (p90) REVERT: A 795 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.7947 (t) REVERT: A 827 ASP cc_start: 0.6923 (m-30) cc_final: 0.6700 (m-30) REVERT: A 844 ASN cc_start: 0.7242 (t0) cc_final: 0.7039 (t0) REVERT: A 880 ASP cc_start: 0.2488 (OUTLIER) cc_final: 0.1423 (t0) REVERT: A 910 LYS cc_start: 0.4344 (mtpt) cc_final: 0.3460 (ttpp) REVERT: A 922 TYR cc_start: 0.7709 (m-80) cc_final: 0.7426 (m-80) REVERT: A 943 ILE cc_start: 0.7690 (mt) cc_final: 0.7332 (mt) REVERT: A 994 MET cc_start: 0.5601 (tpt) cc_final: 0.5161 (tpt) REVERT: A 1036 ASN cc_start: 0.7796 (t0) cc_final: 0.7500 (t0) REVERT: A 1042 SER cc_start: 0.7606 (m) cc_final: 0.7218 (p) REVERT: A 1055 SER cc_start: 0.8422 (p) cc_final: 0.8203 (m) REVERT: A 1061 ILE cc_start: 0.8792 (mt) cc_final: 0.8555 (mt) REVERT: A 1205 MET cc_start: 0.7029 (ttp) cc_final: 0.6719 (ttp) REVERT: C 155 MET cc_start: 0.4806 (mmm) cc_final: 0.4342 (mmm) REVERT: C 174 TRP cc_start: 0.7031 (p-90) cc_final: 0.6434 (p-90) REVERT: C 238 MET cc_start: 0.3611 (ptt) cc_final: 0.3149 (ptt) REVERT: C 615 SER cc_start: 0.8107 (m) cc_final: 0.7410 (t) REVERT: C 623 ASP cc_start: 0.7129 (t0) cc_final: 0.6640 (t0) REVERT: C 646 ASN cc_start: 0.7279 (t0) cc_final: 0.6954 (t0) REVERT: C 647 LEU cc_start: 0.7525 (mt) cc_final: 0.7210 (mp) REVERT: C 744 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5583 (mt) REVERT: C 821 ASN cc_start: 0.7244 (m-40) cc_final: 0.6807 (m-40) REVERT: C 828 LEU cc_start: 0.8145 (tp) cc_final: 0.7572 (tp) REVERT: C 977 VAL cc_start: 0.7365 (t) cc_final: 0.6483 (m) REVERT: C 990 LEU cc_start: 0.3486 (OUTLIER) cc_final: 0.2713 (tp) REVERT: C 994 MET cc_start: 0.7119 (tpp) cc_final: 0.6358 (tpp) REVERT: C 1026 LEU cc_start: 0.1706 (OUTLIER) cc_final: 0.0352 (tp) REVERT: C 1043 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7650 (tp) REVERT: C 1060 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6975 (tt0) REVERT: C 1071 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7468 (mm-40) REVERT: C 1075 ASP cc_start: 0.7630 (m-30) cc_final: 0.6936 (m-30) REVERT: C 1079 ASN cc_start: 0.8085 (m-40) cc_final: 0.7799 (m110) REVERT: C 1094 SER cc_start: 0.7964 (m) cc_final: 0.7386 (t) REVERT: C 1096 ILE cc_start: 0.8403 (tp) cc_final: 0.8115 (tp) REVERT: B 56 TYR cc_start: 0.7614 (m-80) cc_final: 0.6917 (m-80) REVERT: B 120 GLU cc_start: 0.2343 (mp0) cc_final: 0.1726 (tt0) REVERT: B 155 MET cc_start: 0.5737 (mmm) cc_final: 0.4981 (mmm) REVERT: B 635 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6244 (tm-30) REVERT: B 731 VAL cc_start: 0.7295 (p) cc_final: 0.7069 (t) REVERT: B 806 SER cc_start: 0.7714 (t) cc_final: 0.7447 (m) REVERT: B 955 ILE cc_start: 0.5556 (mt) cc_final: 0.4904 (mt) REVERT: B 967 MET cc_start: 0.3931 (tpp) cc_final: 0.3695 (tpp) REVERT: B 1059 GLN cc_start: 0.7348 (tp-100) cc_final: 0.6945 (tp-100) REVERT: B 1195 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6162 (mm-30) REVERT: B 1205 MET cc_start: 0.3183 (mpp) cc_final: 0.2873 (mpp) REVERT: B 1214 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6694 (tmtm) outliers start: 111 outliers final: 72 residues processed: 507 average time/residue: 0.4053 time to fit residues: 336.7420 Evaluate side-chains 507 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 424 time to evaluate : 2.967 ------------------------------------------------------------------------------- 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 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 880 ASP 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 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 267 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 317 VAL 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 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 676 ARG 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 764 PHE Chi-restraints excluded: chain C residue 990 LEU 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 1043 LEU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1131 LEU 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 44 LEU 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 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 853 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 909 ASN 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 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1089 VAL 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 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 8 optimal weight: 3.9990 chunk 340 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 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** A 703 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.230539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.189013 restraints weight = 63203.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.195539 restraints weight = 35339.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.198450 restraints weight = 19633.935| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28478 Z= 0.166 Angle : 0.575 15.076 38867 Z= 0.302 Chirality : 0.044 0.261 4389 Planarity : 0.004 0.055 4991 Dihedral : 5.135 57.364 4010 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.61 % Allowed : 13.64 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3545 helix: 0.91 (0.19), residues: 739 sheet: -0.51 (0.20), residues: 679 loop : -2.19 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 971 HIS 0.005 0.001 HIS B 826 PHE 0.027 0.002 PHE C1143 TYR 0.030 0.001 TYR A 641 ARG 0.010 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 1.72492 ( 18) hydrogen bonds : bond 0.04217 ( 948) hydrogen bonds : angle 5.00508 ( 2757) SS BOND : bond 0.00283 ( 67) SS BOND : angle 1.22426 ( 134) covalent geometry : bond 0.00359 (28405) covalent geometry : angle 0.56998 (38715) *********************** 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 543 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 430 time to evaluate : 2.720 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 105 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7213 (ttpt) REVERT: A 155 MET cc_start: 0.4205 (mmm) cc_final: 0.3702 (mmm) REVERT: A 186 LYS cc_start: 0.5695 (mmmm) cc_final: 0.5434 (mmmt) REVERT: A 213 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5886 (t80) REVERT: A 218 MET cc_start: 0.6784 (ttm) cc_final: 0.6439 (ttm) REVERT: A 236 TYR cc_start: 0.6937 (t80) cc_final: 0.6421 (t80) REVERT: A 387 THR cc_start: 0.3049 (OUTLIER) cc_final: 0.2515 (p) REVERT: A 683 GLN cc_start: 0.5966 (tm-30) cc_final: 0.5661 (tm-30) REVERT: A 702 ASN cc_start: 0.7670 (t0) cc_final: 0.7339 (t0) REVERT: A 746 TYR cc_start: 0.6465 (t80) cc_final: 0.5818 (t80) REVERT: A 780 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5343 (mp0) REVERT: A 794 PHE cc_start: 0.6918 (p90) cc_final: 0.6538 (p90) REVERT: A 795 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8002 (t) REVERT: A 827 ASP cc_start: 0.6892 (m-30) cc_final: 0.6673 (m-30) REVERT: A 880 ASP cc_start: 0.2493 (OUTLIER) cc_final: 0.1394 (t0) REVERT: A 910 LYS cc_start: 0.4475 (mtpt) cc_final: 0.3423 (ttpp) REVERT: A 922 TYR cc_start: 0.7686 (m-80) cc_final: 0.7408 (m-80) REVERT: A 943 ILE cc_start: 0.7642 (mt) cc_final: 0.7318 (mt) REVERT: A 994 MET cc_start: 0.5503 (tpt) cc_final: 0.5098 (tpt) REVERT: A 1036 ASN cc_start: 0.7839 (t0) cc_final: 0.7549 (t0) REVERT: A 1042 SER cc_start: 0.7578 (m) cc_final: 0.7211 (p) REVERT: A 1205 MET cc_start: 0.6977 (ttp) cc_final: 0.6710 (ttp) REVERT: C 174 TRP cc_start: 0.7007 (p-90) cc_final: 0.6463 (p-90) REVERT: C 238 MET cc_start: 0.3669 (ptt) cc_final: 0.3216 (ptt) REVERT: C 281 ASP cc_start: 0.5933 (t70) cc_final: 0.5671 (t70) REVERT: C 615 SER cc_start: 0.8091 (m) cc_final: 0.7389 (t) REVERT: C 623 ASP cc_start: 0.7125 (t0) cc_final: 0.6659 (t0) REVERT: C 646 ASN cc_start: 0.7308 (t0) cc_final: 0.7013 (t0) REVERT: C 647 LEU cc_start: 0.7553 (mt) cc_final: 0.7250 (mp) REVERT: C 744 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5563 (mt) REVERT: C 821 ASN cc_start: 0.7289 (m-40) cc_final: 0.6828 (m-40) REVERT: C 977 VAL cc_start: 0.7425 (t) cc_final: 0.6563 (m) REVERT: C 990 LEU cc_start: 0.3534 (OUTLIER) cc_final: 0.2788 (tp) REVERT: C 994 MET cc_start: 0.7099 (tpp) cc_final: 0.6375 (tpp) REVERT: C 1026 LEU cc_start: 0.1583 (OUTLIER) cc_final: 0.0177 (tp) REVERT: C 1036 ASN cc_start: 0.7792 (m-40) cc_final: 0.7203 (t0) REVERT: C 1050 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7617 (mtmt) REVERT: C 1060 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 1071 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7693 (mm-40) REVERT: C 1077 LEU cc_start: 0.8140 (tp) cc_final: 0.7920 (tt) REVERT: C 1079 ASN cc_start: 0.7972 (m-40) cc_final: 0.7694 (m-40) REVERT: C 1094 SER cc_start: 0.7952 (m) cc_final: 0.7382 (t) REVERT: C 1191 TYR cc_start: 0.5914 (t80) cc_final: 0.5168 (t80) REVERT: B 56 TYR cc_start: 0.7606 (m-80) cc_final: 0.6872 (m-10) REVERT: B 120 GLU cc_start: 0.2533 (mp0) cc_final: 0.2116 (tt0) REVERT: B 155 MET cc_start: 0.5719 (mmm) cc_final: 0.4968 (mmm) REVERT: B 264 ARG cc_start: 0.6908 (ptp-170) cc_final: 0.6514 (ptp90) REVERT: B 635 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6189 (tm-30) REVERT: B 731 VAL cc_start: 0.7347 (p) cc_final: 0.7131 (t) REVERT: B 806 SER cc_start: 0.7650 (t) cc_final: 0.7411 (m) REVERT: B 949 ILE cc_start: 0.7549 (pt) cc_final: 0.7111 (tp) REVERT: B 955 ILE cc_start: 0.5445 (mt) cc_final: 0.4802 (mt) REVERT: B 967 MET cc_start: 0.3937 (tpp) cc_final: 0.3723 (tpp) REVERT: B 1057 SER cc_start: 0.8663 (t) cc_final: 0.8285 (p) REVERT: B 1059 GLN cc_start: 0.7362 (tp-100) cc_final: 0.7115 (tp40) REVERT: B 1064 ARG cc_start: 0.6916 (mtm110) cc_final: 0.6633 (mtt90) REVERT: B 1073 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6862 (mt0) REVERT: B 1077 LEU cc_start: 0.8844 (mt) cc_final: 0.8530 (mp) REVERT: B 1195 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6213 (mm-30) REVERT: B 1214 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6712 (tmtm) outliers start: 113 outliers final: 82 residues processed: 505 average time/residue: 0.3618 time to fit residues: 293.7341 Evaluate side-chains 511 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 420 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 275 VAL 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 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 880 ASP 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 317 VAL 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 622 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 ILE 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 748 LEU Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 990 LEU 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 1043 LEU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1131 LEU 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 44 LEU 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 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 759 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 818 VAL 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 909 ASN 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 1020 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1089 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 248 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 257 optimal weight: 0.3980 chunk 145 optimal weight: 0.9990 chunk 298 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 153 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.233953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.193577 restraints weight = 64312.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.200297 restraints weight = 35595.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.203438 restraints weight = 20163.451| |-----------------------------------------------------------------------------| r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28478 Z= 0.104 Angle : 0.538 12.499 38867 Z= 0.278 Chirality : 0.043 0.422 4389 Planarity : 0.004 0.080 4991 Dihedral : 4.916 57.682 4010 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.04 % Allowed : 14.28 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3545 helix: 1.27 (0.20), residues: 746 sheet: -0.25 (0.20), residues: 655 loop : -2.07 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 971 HIS 0.003 0.000 HIS C 160 PHE 0.024 0.001 PHE B 368 TYR 0.027 0.001 TYR A 641 ARG 0.006 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 1.65963 ( 18) hydrogen bonds : bond 0.03530 ( 948) hydrogen bonds : angle 4.73933 ( 2757) SS BOND : bond 0.00220 ( 67) SS BOND : angle 1.07785 ( 134) covalent geometry : bond 0.00235 (28405) covalent geometry : angle 0.53409 (38715) *********************** 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 511 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 416 time to evaluate : 2.950 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 105 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7162 (ttpt) REVERT: A 155 MET cc_start: 0.3815 (mmm) cc_final: 0.3338 (mmm) REVERT: A 213 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5645 (t80) REVERT: A 218 MET cc_start: 0.6746 (ttm) cc_final: 0.6349 (ttm) REVERT: A 236 TYR cc_start: 0.6834 (t80) cc_final: 0.6331 (t80) REVERT: A 287 LEU cc_start: 0.7934 (tp) cc_final: 0.7687 (tt) REVERT: A 387 THR cc_start: 0.3052 (OUTLIER) cc_final: 0.2504 (p) REVERT: A 624 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5321 (pp) REVERT: A 659 LYS cc_start: 0.6281 (tttm) cc_final: 0.6062 (tttm) REVERT: A 683 GLN cc_start: 0.6020 (tm-30) cc_final: 0.5716 (tm-30) REVERT: A 702 ASN cc_start: 0.7639 (t0) cc_final: 0.7355 (t0) REVERT: A 746 TYR cc_start: 0.6418 (t80) cc_final: 0.5946 (t80) REVERT: A 794 PHE cc_start: 0.6754 (p90) cc_final: 0.6457 (p90) REVERT: A 795 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7872 (t) REVERT: A 827 ASP cc_start: 0.6919 (m-30) cc_final: 0.6654 (m-30) REVERT: A 867 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4691 (mt) REVERT: A 910 LYS cc_start: 0.4480 (mtpt) cc_final: 0.3478 (tttm) REVERT: A 922 TYR cc_start: 0.7543 (m-80) cc_final: 0.7293 (m-80) REVERT: A 943 ILE cc_start: 0.7505 (mt) cc_final: 0.7147 (mt) REVERT: A 994 MET cc_start: 0.5517 (tpt) cc_final: 0.5098 (tpt) REVERT: A 1036 ASN cc_start: 0.7816 (t0) cc_final: 0.7472 (t0) REVERT: A 1042 SER cc_start: 0.7593 (m) cc_final: 0.7212 (p) REVERT: A 1076 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7912 (mtm-85) REVERT: A 1115 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.4456 (mttp) REVERT: A 1205 MET cc_start: 0.6915 (ttp) cc_final: 0.6690 (ttp) REVERT: C 155 MET cc_start: 0.3777 (mmm) cc_final: 0.2904 (mmm) REVERT: C 174 TRP cc_start: 0.6759 (p-90) cc_final: 0.6111 (p-90) REVERT: C 238 MET cc_start: 0.3611 (ptt) cc_final: 0.3122 (ptt) REVERT: C 281 ASP cc_start: 0.5841 (t70) cc_final: 0.5515 (t70) REVERT: C 615 SER cc_start: 0.8051 (m) cc_final: 0.7350 (t) REVERT: C 646 ASN cc_start: 0.7129 (t0) cc_final: 0.6789 (t0) REVERT: C 647 LEU cc_start: 0.7382 (mt) cc_final: 0.7045 (mp) REVERT: C 821 ASN cc_start: 0.7210 (m-40) cc_final: 0.6881 (m110) REVERT: C 822 TYR cc_start: 0.6710 (m-80) cc_final: 0.5768 (m-80) REVERT: C 857 VAL cc_start: 0.7865 (t) cc_final: 0.7434 (m) REVERT: C 977 VAL cc_start: 0.7350 (t) cc_final: 0.6537 (m) REVERT: C 990 LEU cc_start: 0.3668 (OUTLIER) cc_final: 0.2951 (tp) REVERT: C 994 MET cc_start: 0.7029 (tpp) cc_final: 0.6331 (tpp) REVERT: C 1020 THR cc_start: 0.7734 (p) cc_final: 0.7530 (p) REVERT: C 1036 ASN cc_start: 0.7752 (m-40) cc_final: 0.7166 (t0) REVERT: C 1043 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7583 (tp) REVERT: C 1050 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7581 (mtmt) REVERT: C 1060 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6835 (tt0) REVERT: C 1079 ASN cc_start: 0.8003 (m-40) cc_final: 0.7634 (m-40) REVERT: C 1094 SER cc_start: 0.7936 (m) cc_final: 0.7356 (t) REVERT: C 1191 TYR cc_start: 0.5869 (t80) cc_final: 0.5105 (t80) REVERT: B 56 TYR cc_start: 0.7541 (m-80) cc_final: 0.6799 (m-80) REVERT: B 120 GLU cc_start: 0.2447 (mp0) cc_final: 0.2147 (tt0) REVERT: B 140 GLN cc_start: 0.7318 (pp30) cc_final: 0.6951 (pp30) REVERT: B 155 MET cc_start: 0.5348 (mmm) cc_final: 0.4676 (mmm) REVERT: B 232 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7720 (tp) REVERT: B 264 ARG cc_start: 0.6810 (ptp-170) cc_final: 0.6461 (ptp90) REVERT: B 635 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6149 (tm-30) REVERT: B 820 SER cc_start: 0.7790 (t) cc_final: 0.7571 (m) REVERT: B 955 ILE cc_start: 0.5206 (mt) cc_final: 0.4692 (mt) REVERT: B 1057 SER cc_start: 0.8718 (t) cc_final: 0.8344 (p) REVERT: B 1059 GLN cc_start: 0.7251 (tp-100) cc_final: 0.7001 (tp40) REVERT: B 1064 ARG cc_start: 0.6863 (mtm110) cc_final: 0.6625 (mtm110) REVERT: B 1073 GLN cc_start: 0.7281 (mm-40) cc_final: 0.6803 (mt0) REVERT: B 1195 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6163 (mm-30) REVERT: B 1205 MET cc_start: 0.3210 (mpp) cc_final: 0.2973 (mpp) REVERT: B 1214 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6728 (tmtm) outliers start: 95 outliers final: 67 residues processed: 477 average time/residue: 0.3717 time to fit residues: 284.3485 Evaluate side-chains 485 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 408 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 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 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 867 LEU 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 1069 GLU 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 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 317 VAL 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 632 ILE 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 990 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1043 LEU 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 44 LEU 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 232 LEU Chi-restraints excluded: chain B residue 245 ILE 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 909 ASN 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 1020 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1089 VAL 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 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 247 optimal weight: 5.9990 chunk 278 optimal weight: 0.0030 chunk 163 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 241 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 40.0000 chunk 297 optimal weight: 3.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- 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 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN B1045 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.230116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188748 restraints weight = 63606.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.196215 restraints weight = 34643.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.197546 restraints weight = 19932.590| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28478 Z= 0.161 Angle : 0.593 12.387 38867 Z= 0.309 Chirality : 0.045 0.359 4389 Planarity : 0.004 0.066 4991 Dihedral : 5.123 57.897 4005 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.00 % Allowed : 14.60 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3545 helix: 0.98 (0.19), residues: 746 sheet: -0.39 (0.20), residues: 667 loop : -2.11 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 971 HIS 0.004 0.001 HIS B 826 PHE 0.028 0.002 PHE B 202 TYR 0.024 0.001 TYR B 203 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 6) link_NAG-ASN : angle 1.75149 ( 18) hydrogen bonds : bond 0.04151 ( 948) hydrogen bonds : angle 5.04154 ( 2757) SS BOND : bond 0.00291 ( 67) SS BOND : angle 1.36954 ( 134) covalent geometry : bond 0.00355 (28405) covalent geometry : angle 0.58723 (38715) *********************** 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 521 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 427 time to evaluate : 2.749 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: A 105 LYS cc_start: 0.7599 (ttpt) cc_final: 0.7132 (ttpt) REVERT: A 155 MET cc_start: 0.4356 (mmm) cc_final: 0.3797 (mmm) REVERT: A 213 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5877 (t80) REVERT: A 218 MET cc_start: 0.6776 (ttm) cc_final: 0.6398 (ttm) REVERT: A 236 TYR cc_start: 0.6912 (t80) cc_final: 0.6366 (t80) REVERT: A 287 LEU cc_start: 0.8146 (tp) cc_final: 0.7885 (tt) REVERT: A 387 THR cc_start: 0.3162 (OUTLIER) cc_final: 0.2641 (p) REVERT: A 624 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5390 (pp) REVERT: A 683 GLN cc_start: 0.6105 (tm-30) cc_final: 0.5770 (tm-30) REVERT: A 702 ASN cc_start: 0.7753 (t0) cc_final: 0.7432 (t0) REVERT: A 746 TYR cc_start: 0.6757 (t80) cc_final: 0.6065 (t80) REVERT: A 794 PHE cc_start: 0.6937 (p90) cc_final: 0.6577 (p90) REVERT: A 795 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7926 (t) REVERT: A 827 ASP cc_start: 0.6984 (m-30) cc_final: 0.6762 (m-30) REVERT: A 867 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5171 (mp) REVERT: A 880 ASP cc_start: 0.2388 (OUTLIER) cc_final: 0.1240 (t0) REVERT: A 910 LYS cc_start: 0.4717 (mtpt) cc_final: 0.3559 (mttt) REVERT: A 922 TYR cc_start: 0.7730 (m-80) cc_final: 0.7423 (m-80) REVERT: A 943 ILE cc_start: 0.7632 (mt) cc_final: 0.7330 (mt) REVERT: A 994 MET cc_start: 0.5610 (tpt) cc_final: 0.5189 (tpt) REVERT: A 1036 ASN cc_start: 0.7930 (t0) cc_final: 0.7589 (t0) REVERT: A 1042 SER cc_start: 0.7586 (m) cc_final: 0.7239 (p) REVERT: A 1076 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7956 (mtm-85) REVERT: A 1115 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.4821 (mttm) REVERT: A 1205 MET cc_start: 0.6897 (ttp) cc_final: 0.6666 (ttp) REVERT: C 56 TYR cc_start: 0.6223 (m-80) cc_final: 0.5932 (m-80) REVERT: C 155 MET cc_start: 0.3983 (mmm) cc_final: 0.3079 (mmm) REVERT: C 164 LYS cc_start: 0.5795 (mmtt) cc_final: 0.5580 (mmtt) REVERT: C 174 TRP cc_start: 0.6712 (p-90) cc_final: 0.6086 (p-90) REVERT: C 281 ASP cc_start: 0.5682 (t70) cc_final: 0.5452 (t70) REVERT: C 615 SER cc_start: 0.8114 (m) cc_final: 0.7424 (t) REVERT: C 646 ASN cc_start: 0.7300 (t0) cc_final: 0.6977 (t0) REVERT: C 647 LEU cc_start: 0.7550 (mt) cc_final: 0.7232 (mp) REVERT: C 669 ILE cc_start: 0.8324 (mm) cc_final: 0.8013 (mm) REVERT: C 821 ASN cc_start: 0.7256 (m-40) cc_final: 0.6801 (m-40) REVERT: C 977 VAL cc_start: 0.7354 (t) cc_final: 0.6421 (m) REVERT: C 990 LEU cc_start: 0.3496 (OUTLIER) cc_final: 0.2709 (mp) REVERT: C 994 MET cc_start: 0.7136 (tpp) cc_final: 0.6467 (tpp) REVERT: C 1026 LEU cc_start: 0.1708 (OUTLIER) cc_final: 0.0306 (tp) REVERT: C 1036 ASN cc_start: 0.7922 (m-40) cc_final: 0.7362 (t0) REVERT: C 1050 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7661 (mtmt) REVERT: C 1060 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6962 (tt0) REVERT: C 1071 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7525 (mm110) REVERT: C 1079 ASN cc_start: 0.8005 (m-40) cc_final: 0.7674 (m-40) REVERT: C 1094 SER cc_start: 0.7921 (m) cc_final: 0.7338 (t) REVERT: C 1191 TYR cc_start: 0.5902 (t80) cc_final: 0.5125 (t80) REVERT: B 56 TYR cc_start: 0.7580 (m-80) cc_final: 0.6836 (m-10) REVERT: B 140 GLN cc_start: 0.7390 (pp30) cc_final: 0.6786 (pp30) REVERT: B 155 MET cc_start: 0.5760 (mmm) cc_final: 0.4984 (mmm) REVERT: B 166 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8306 (ttpt) REVERT: B 232 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 635 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6193 (tm-30) REVERT: B 806 SER cc_start: 0.7662 (t) cc_final: 0.7445 (m) REVERT: B 820 SER cc_start: 0.7956 (t) cc_final: 0.7718 (m) REVERT: B 949 ILE cc_start: 0.7573 (pt) cc_final: 0.7111 (tp) REVERT: B 1059 GLN cc_start: 0.7369 (tp-100) cc_final: 0.7132 (tp40) REVERT: B 1064 ARG cc_start: 0.6984 (mtm110) cc_final: 0.6718 (mtm110) REVERT: B 1073 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6913 (mt0) REVERT: B 1077 LEU cc_start: 0.8860 (mt) cc_final: 0.8533 (mp) REVERT: B 1195 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6200 (mm-30) REVERT: B 1205 MET cc_start: 0.3237 (mpp) cc_final: 0.3029 (mpp) REVERT: B 1214 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6744 (tmtm) outliers start: 94 outliers final: 72 residues processed: 486 average time/residue: 0.3621 time to fit residues: 283.8375 Evaluate side-chains 502 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 419 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 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 711 PHE Chi-restraints excluded: chain A residue 719 CYS 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 867 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 1064 ARG Chi-restraints excluded: chain A residue 1069 GLU 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 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 317 VAL 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 632 ILE 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 990 LEU 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 1131 LEU 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 44 LEU 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 232 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 309 PHE 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 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 1020 THR Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1089 VAL 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 1208 CYS 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 43 optimal weight: 0.0010 chunk 230 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 338 optimal weight: 0.0980 chunk 54 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 854 GLN ** 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 = 0.4849 r_free = 0.4849 target = 0.233505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.192595 restraints weight = 64561.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.199044 restraints weight = 35922.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.201398 restraints weight = 22934.931| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28478 Z= 0.109 Angle : 0.559 11.405 38867 Z= 0.287 Chirality : 0.043 0.285 4389 Planarity : 0.004 0.061 4991 Dihedral : 4.931 59.917 4004 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.56 % Allowed : 15.21 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3545 helix: 1.24 (0.20), residues: 753 sheet: -0.21 (0.20), residues: 662 loop : -2.00 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 971 HIS 0.009 0.001 HIS C1129 PHE 0.026 0.001 PHE B 202 TYR 0.018 0.001 TYR B1148 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 6) link_NAG-ASN : angle 1.69420 ( 18) hydrogen bonds : bond 0.03550 ( 948) hydrogen bonds : angle 4.74126 ( 2757) SS BOND : bond 0.00213 ( 67) SS BOND : angle 1.12688 ( 134) covalent geometry : bond 0.00246 (28405) covalent geometry : angle 0.55514 (38715) ********************** 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 496 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 416 time to evaluate : 3.005 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: A 105 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7130 (ttpt) REVERT: A 155 MET cc_start: 0.4067 (mmm) cc_final: 0.3556 (mmm) REVERT: A 213 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5641 (t80) REVERT: A 218 MET cc_start: 0.6812 (ttm) cc_final: 0.6443 (ttm) REVERT: A 236 TYR cc_start: 0.6898 (t80) cc_final: 0.6404 (t80) REVERT: A 287 LEU cc_start: 0.8014 (tp) cc_final: 0.7734 (tt) REVERT: A 387 THR cc_start: 0.3079 (OUTLIER) cc_final: 0.2543 (p) REVERT: A 624 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5351 (pp) REVERT: A 683 GLN cc_start: 0.6096 (tm-30) cc_final: 0.5767 (tm-30) REVERT: A 702 ASN cc_start: 0.7575 (t0) cc_final: 0.7282 (t0) REVERT: A 746 TYR cc_start: 0.6727 (t80) cc_final: 0.6104 (t80) REVERT: A 794 PHE cc_start: 0.6842 (p90) cc_final: 0.6452 (p90) REVERT: A 795 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 827 ASP cc_start: 0.7025 (m-30) cc_final: 0.6780 (m-30) REVERT: A 867 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.5204 (mt) REVERT: A 880 ASP cc_start: 0.2361 (OUTLIER) cc_final: 0.1272 (t0) REVERT: A 910 LYS cc_start: 0.4610 (mtpt) cc_final: 0.4008 (ttmm) REVERT: A 922 TYR cc_start: 0.7637 (m-80) cc_final: 0.7359 (m-80) REVERT: A 994 MET cc_start: 0.5526 (tpt) cc_final: 0.5102 (tpt) REVERT: A 1036 ASN cc_start: 0.7867 (t0) cc_final: 0.7509 (t0) REVERT: A 1042 SER cc_start: 0.7524 (m) cc_final: 0.7187 (p) REVERT: A 1076 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7955 (mtm-85) REVERT: A 1115 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4355 (mttm) REVERT: C 155 MET cc_start: 0.3659 (mmm) cc_final: 0.2604 (mmm) REVERT: C 281 ASP cc_start: 0.5682 (t70) cc_final: 0.5411 (t70) REVERT: C 615 SER cc_start: 0.8121 (m) cc_final: 0.7443 (t) REVERT: C 647 LEU cc_start: 0.7356 (mt) cc_final: 0.6985 (mp) REVERT: C 669 ILE cc_start: 0.8347 (mm) cc_final: 0.8039 (mm) REVERT: C 821 ASN cc_start: 0.7213 (m-40) cc_final: 0.6871 (m110) REVERT: C 822 TYR cc_start: 0.6726 (m-80) cc_final: 0.5732 (m-80) REVERT: C 857 VAL cc_start: 0.7885 (t) cc_final: 0.7443 (m) REVERT: C 977 VAL cc_start: 0.7311 (t) cc_final: 0.6452 (m) REVERT: C 990 LEU cc_start: 0.3853 (OUTLIER) cc_final: 0.3086 (mp) REVERT: C 994 MET cc_start: 0.7042 (tpp) cc_final: 0.6390 (tpp) REVERT: C 1036 ASN cc_start: 0.7907 (m-40) cc_final: 0.7357 (t0) REVERT: C 1050 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7520 (mtmt) REVERT: C 1060 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6864 (tt0) REVERT: C 1071 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7511 (mm-40) REVERT: C 1079 ASN cc_start: 0.7956 (m-40) cc_final: 0.7640 (m-40) REVERT: C 1094 SER cc_start: 0.7860 (m) cc_final: 0.7284 (t) REVERT: C 1191 TYR cc_start: 0.5841 (t80) cc_final: 0.5108 (t80) REVERT: B 56 TYR cc_start: 0.7541 (m-80) cc_final: 0.6806 (m-80) REVERT: B 140 GLN cc_start: 0.7322 (pp30) cc_final: 0.6694 (pp30) REVERT: B 155 MET cc_start: 0.5371 (mmm) cc_final: 0.4681 (mmm) REVERT: B 232 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 635 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6081 (tm-30) REVERT: B 820 SER cc_start: 0.7896 (t) cc_final: 0.7631 (m) REVERT: B 944 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7581 (ttmm) REVERT: B 955 ILE cc_start: 0.5246 (mt) cc_final: 0.4725 (mt) REVERT: B 1059 GLN cc_start: 0.7271 (tp-100) cc_final: 0.7017 (tp40) REVERT: B 1064 ARG cc_start: 0.6956 (mtm110) cc_final: 0.6694 (mtm110) REVERT: B 1073 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6890 (mt0) REVERT: B 1195 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6199 (mm-30) REVERT: B 1214 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6772 (tmtm) outliers start: 80 outliers final: 64 residues processed: 468 average time/residue: 0.3817 time to fit residues: 287.5396 Evaluate side-chains 481 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 406 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 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 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 867 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 1069 GLU 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 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 317 VAL 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 632 ILE Chi-restraints excluded: chain C residue 663 THR 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 990 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 B residue 44 LEU 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 232 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 309 PHE 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 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 1020 THR Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1089 VAL 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 1208 CYS 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 138 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** A1111 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.227830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.185978 restraints weight = 62978.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.191533 restraints weight = 35715.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.193693 restraints weight = 22182.463| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 28478 Z= 0.287 Angle : 0.727 10.383 38867 Z= 0.387 Chirality : 0.049 0.339 4389 Planarity : 0.005 0.068 4991 Dihedral : 5.731 59.384 4004 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.75 % Allowed : 15.27 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3545 helix: 0.34 (0.19), residues: 732 sheet: -0.68 (0.20), residues: 696 loop : -2.08 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 971 HIS 0.009 0.001 HIS B 826 PHE 0.037 0.002 PHE A 67 TYR 0.036 0.002 TYR B 203 ARG 0.006 0.001 ARG B 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 6) link_NAG-ASN : angle 2.11156 ( 18) hydrogen bonds : bond 0.05434 ( 948) hydrogen bonds : angle 5.59248 ( 2757) SS BOND : bond 0.00454 ( 67) SS BOND : angle 1.46252 ( 134) covalent geometry : bond 0.00610 (28405) covalent geometry : angle 0.72219 (38715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10558.04 seconds wall clock time: 185 minutes 5.22 seconds (11105.22 seconds total)