Starting phenix.real_space_refine on Sat Jul 4 19:12:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dt8_27692/07_2026/8dt8_27692.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 108 5.16 5 C 14506 2.51 5 N 3775 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "H" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 982 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "C" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6377 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 43, 'TRANS': 774} Chain breaks: 8 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6375 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 45, 'TRANS': 772} Chain breaks: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 3 Time building chain proxies: 4.63, per 1000 atoms: 0.20 Number of scatterers: 22796 At special positions: 0 Unit cell: (140.03, 136.895, 204.82, 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 108 16.00 O 4407 8.00 N 3775 7.00 C 14506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.90 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 69 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 69 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 331 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A1098 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C1098 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 910.4 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 43 sheets defined 24.0% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.373A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.081A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.745A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.018A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.016A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.720A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.886A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.064A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.440A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.194A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.784A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.050A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.719A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.495A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.394A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.538A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.806A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 7 through 8 removed outlier: 3.553A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP H 100I" --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.373A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.763A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.588A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.770A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.539A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.265A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AD4, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AD5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.176A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.765A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.009A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.312A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.691A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.337A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.553A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7330 1.35 - 1.47: 5860 1.47 - 1.59: 9978 1.59 - 1.72: 0 1.72 - 1.84: 137 Bond restraints: 23305 Sorted by residual: bond pdb=" N PRO B 986 " pdb=" CA PRO B 986 " ideal model delta sigma weight residual 1.465 1.506 -0.041 2.03e-02 2.43e+03 4.10e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU A 916 " pdb=" CD2 LEU A 916 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 ... (remaining 23300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 29742 1.89 - 3.77: 1677 3.77 - 5.66: 259 5.66 - 7.55: 19 7.55 - 9.44: 3 Bond angle restraints: 31700 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.13 -5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 111.28 116.13 -4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 110.80 120.24 -9.44 2.13e+00 2.20e-01 1.96e+01 angle pdb=" N LEU A 117 " pdb=" CA LEU A 117 " pdb=" C LEU A 117 " ideal model delta sigma weight residual 109.46 116.16 -6.70 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.50 -4.80 1.22e+00 6.72e-01 1.55e+01 ... (remaining 31695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 13243 17.43 - 34.86: 397 34.86 - 52.28: 91 52.28 - 69.71: 59 69.71 - 87.14: 20 Dihedral angle restraints: 13810 sinusoidal: 5394 harmonic: 8416 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -160.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 37.28 55.72 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 136.09 -43.09 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 13807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2266 0.045 - 0.089: 948 0.089 - 0.134: 320 0.134 - 0.178: 83 0.178 - 0.223: 14 Chirality restraints: 3631 Sorted by residual: chirality pdb=" CA PHE D 67 " pdb=" N PHE D 67 " pdb=" C PHE D 67 " pdb=" CB PHE D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 945 " pdb=" CB LEU B 945 " pdb=" CD1 LEU B 945 " pdb=" CD2 LEU B 945 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3628 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 954 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLN B 954 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN B 954 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1098 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C1098 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN C1098 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C1099 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 948 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU A 948 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU A 948 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN A 949 " 0.022 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 275 2.65 - 3.21: 20001 3.21 - 3.77: 34691 3.77 - 4.34: 49382 4.34 - 4.90: 81618 Nonbonded interactions: 185967 Sorted by model distance: nonbonded pdb=" O THR C 108 " pdb=" OG1 THR C 236 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 158 " model vdw 2.161 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR C1077 " pdb=" O PHE C1095 " model vdw 2.293 3.040 ... (remaining 185962 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 'B' and resid 28 through 1303) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 1144 or resid 1302 through 1304)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100H through 112)) selection = (chain 'H' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100J through 112)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.130 23355 Z= 0.248 Angle : 1.043 53.787 31813 Z= 0.599 Chirality : 0.056 0.223 3631 Planarity : 0.006 0.039 4102 Dihedral : 10.654 87.138 8281 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.20 % Allowed : 1.06 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 2844 helix: 1.11 (0.19), residues: 603 sheet: 1.06 (0.20), residues: 628 loop : -0.00 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 71 TYR 0.047 0.003 TYR H 100D PHE 0.031 0.002 PHE B 133 TRP 0.023 0.003 TRP H 47 HIS 0.009 0.002 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (23305) covalent geometry : angle 0.97387 / 0.57 (31700) SS BOND : bond 0.02216 / 1.19 ( 37) SS BOND : angle 7.70451 / 5.17 ( 74) hydrogen bonds : bond 0.13236 / 8.34 ( 997) hydrogen bonds : angle 7.63291 / 5.37 ( 2841) link_NAG-ASN : bond 0.00204 / 0.14 ( 13) link_NAG-ASN : angle 2.15956 / 1.56 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 464 time to evaluate : 0.898 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 141 LEU cc_start: 0.5993 (mt) cc_final: 0.5171 (tp) REVERT: A 153 MET cc_start: 0.2745 (tpt) cc_final: 0.2174 (ptp) REVERT: A 558 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7596 (ptpt) REVERT: A 581 THR cc_start: 0.8104 (m) cc_final: 0.7878 (p) REVERT: H 32 TYR cc_start: 0.4590 (m-80) cc_final: 0.4185 (m-10) REVERT: H 58 TYR cc_start: 0.7677 (t80) cc_final: 0.7439 (t80) REVERT: H 89 VAL cc_start: 0.7162 (t) cc_final: 0.6701 (p) REVERT: D 36 TRP cc_start: 0.7023 (m100) cc_final: 0.5628 (m100) REVERT: D 37 TYR cc_start: 0.7727 (m-80) cc_final: 0.7490 (m-80) REVERT: D 71 ARG cc_start: 0.6846 (ppt90) cc_final: 0.6415 (ptt90) REVERT: D 78 LEU cc_start: 0.7706 (tp) cc_final: 0.5927 (tp) REVERT: D 80 LEU cc_start: 0.7754 (tt) cc_final: 0.7028 (tt) REVERT: C 153 MET cc_start: 0.5757 (mmm) cc_final: 0.4589 (ttt) REVERT: C 190 ARG cc_start: 0.5692 (mtm-85) cc_final: 0.5488 (tpp80) REVERT: C 266 TYR cc_start: 0.6592 (m-80) cc_final: 0.6187 (m-10) REVERT: C 539 VAL cc_start: 0.8190 (t) cc_final: 0.7896 (p) REVERT: C 646 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6659 (tpt90) REVERT: C 856 ASN cc_start: 0.7230 (m-40) cc_final: 0.6921 (p0) REVERT: B 102 ARG cc_start: 0.6856 (mtt180) cc_final: 0.6636 (mtp180) REVERT: B 761 THR cc_start: 0.8528 (m) cc_final: 0.8302 (p) REVERT: B 1029 MET cc_start: 0.8891 (tpp) cc_final: 0.8595 (tpp) outliers start: 5 outliers final: 3 residues processed: 467 average time/residue: 0.1771 time to fit residues: 123.6345 Evaluate side-chains 213 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 GLN A 955 ASN H 82AASN C 245 HIS C 532 ASN C 655 HIS C 926 GLN C 935 GLN C1010 GLN C1101 HIS B 81 ASN B 165 ASN B 188 ASN B 239 GLN B 655 HIS B1048 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073623 restraints weight = 53057.526| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.33 r_work: 0.2931 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 23355 Z= 0.244 Angle : 0.672 13.693 31813 Z= 0.358 Chirality : 0.048 0.377 3631 Planarity : 0.005 0.042 4102 Dihedral : 5.059 59.641 3101 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.81 % Allowed : 5.20 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 2844 helix: 2.41 (0.20), residues: 607 sheet: 0.97 (0.19), residues: 655 loop : -0.32 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 346 TYR 0.023 0.002 TYR A1067 PHE 0.022 0.002 PHE B 133 TRP 0.015 0.002 TRP A 353 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (23305) covalent geometry : angle 0.66334 / 0.36 (31700) SS BOND : bond 0.00937 / 0.55 ( 37) SS BOND : angle 1.73052 / 1.14 ( 74) hydrogen bonds : bond 0.05196 / 3.40 ( 997) hydrogen bonds : angle 6.09433 / 4.30 ( 2841) link_NAG-ASN : bond 0.00510 / 0.32 ( 13) link_NAG-ASN : angle 2.18685 / 1.50 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5921 (mt) cc_final: 0.5431 (tp) REVERT: A 153 MET cc_start: 0.2565 (tpt) cc_final: 0.2133 (ptp) REVERT: A 170 TYR cc_start: 0.7271 (t80) cc_final: 0.7064 (t80) REVERT: A 271 GLN cc_start: 0.7827 (mp10) cc_final: 0.7589 (mp10) REVERT: A 558 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7786 (ptpt) REVERT: H 37 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5846 (t80) REVERT: H 96 TYR cc_start: 0.7441 (t80) cc_final: 0.7182 (t80) REVERT: H 100 ARG cc_start: 0.7463 (mpp-170) cc_final: 0.6955 (mpp80) REVERT: D 36 TRP cc_start: 0.6999 (m100) cc_final: 0.6464 (m100) REVERT: D 80 LEU cc_start: 0.7774 (tt) cc_final: 0.7383 (tp) REVERT: D 100 PHE cc_start: 0.8086 (m-10) cc_final: 0.7448 (m-10) REVERT: C 131 CYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3461 (m) REVERT: C 153 MET cc_start: 0.5781 (mmm) cc_final: 0.4590 (ttt) REVERT: C 190 ARG cc_start: 0.5898 (mtm-85) cc_final: 0.5408 (tpp80) REVERT: C 646 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7121 (tpt90) REVERT: B 102 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6996 (mtm-85) REVERT: B 115 GLN cc_start: 0.7392 (mt0) cc_final: 0.7040 (mm-40) REVERT: B 541 PHE cc_start: 0.7135 (p90) cc_final: 0.6884 (p90) REVERT: B 740 MET cc_start: 0.8627 (tpp) cc_final: 0.8278 (tpp) outliers start: 46 outliers final: 26 residues processed: 252 average time/residue: 0.1533 time to fit residues: 60.4339 Evaluate side-chains 188 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 240 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS D 73 ASN D 76 ASN C 81 ASN C 901 GLN C 955 ASN B 165 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073211 restraints weight = 53085.912| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.26 r_work: 0.2915 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23355 Z= 0.218 Angle : 0.616 9.669 31813 Z= 0.325 Chirality : 0.046 0.240 3631 Planarity : 0.004 0.047 4102 Dihedral : 4.868 48.807 3099 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 1.89 % Allowed : 6.78 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 2844 helix: 2.70 (0.20), residues: 607 sheet: 0.83 (0.19), residues: 645 loop : -0.59 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 71 TYR 0.023 0.002 TYR H 100F PHE 0.020 0.002 PHE B 133 TRP 0.018 0.002 TRP D 36 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (23305) covalent geometry : angle 0.60799 / 0.32 (31700) SS BOND : bond 0.00816 / 0.53 ( 37) SS BOND : angle 1.56433 / 1.03 ( 74) hydrogen bonds : bond 0.04818 / 3.15 ( 997) hydrogen bonds : angle 5.77667 / 4.07 ( 2841) link_NAG-ASN : bond 0.00452 / 0.30 ( 13) link_NAG-ASN : angle 2.20108 / 1.51 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.4902 (t0) cc_final: 0.4581 (t0) REVERT: A 141 LEU cc_start: 0.6125 (mt) cc_final: 0.5354 (tp) REVERT: A 153 MET cc_start: 0.3206 (tpt) cc_final: 0.2407 (ptp) REVERT: A 168 PHE cc_start: 0.5003 (t80) cc_final: 0.4737 (t80) REVERT: A 558 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7832 (ptpt) REVERT: H 37 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5728 (t80) REVERT: H 58 TYR cc_start: 0.7969 (t80) cc_final: 0.7521 (t80) REVERT: H 59 TYR cc_start: 0.7224 (m-80) cc_final: 0.6550 (m-80) REVERT: H 96 TYR cc_start: 0.7413 (t80) cc_final: 0.7126 (t80) REVERT: H 100 ARG cc_start: 0.7484 (mpp-170) cc_final: 0.7032 (mpp80) REVERT: D 37 TYR cc_start: 0.8075 (m-80) cc_final: 0.7623 (m-80) REVERT: D 71 ARG cc_start: 0.6229 (ptt90) cc_final: 0.5995 (ptt-90) REVERT: C 81 ASN cc_start: 0.6464 (t0) cc_final: 0.6099 (t0) REVERT: C 117 LEU cc_start: 0.7428 (mp) cc_final: 0.7171 (mt) REVERT: C 131 CYS cc_start: 0.4239 (OUTLIER) cc_final: 0.3471 (m) REVERT: C 153 MET cc_start: 0.5802 (mmm) cc_final: 0.4689 (ttt) REVERT: C 190 ARG cc_start: 0.5799 (mtm-85) cc_final: 0.5019 (tpt-90) REVERT: C 646 ARG cc_start: 0.7740 (tpt90) cc_final: 0.7092 (tpt90) REVERT: B 102 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6915 (mtm-85) REVERT: B 115 GLN cc_start: 0.7507 (mt0) cc_final: 0.7029 (mm-40) outliers start: 48 outliers final: 32 residues processed: 226 average time/residue: 0.1455 time to fit residues: 51.5785 Evaluate side-chains 198 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 192 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 165 optimal weight: 0.0980 chunk 147 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 274 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073309 restraints weight = 52948.376| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.10 r_work: 0.2967 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23355 Z= 0.121 Angle : 0.540 13.569 31813 Z= 0.284 Chirality : 0.043 0.275 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.555 43.332 3097 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 7.49 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 2844 helix: 3.11 (0.20), residues: 598 sheet: 0.72 (0.19), residues: 646 loop : -0.54 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.024 0.001 TYR H 100F PHE 0.020 0.001 PHE B 133 TRP 0.015 0.001 TRP D 36 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (23305) covalent geometry : angle 0.53279 / 0.28 (31700) SS BOND : bond 0.00549 / 0.31 ( 37) SS BOND : angle 1.40847 / 0.96 ( 74) hydrogen bonds : bond 0.04134 / 2.69 ( 997) hydrogen bonds : angle 5.47949 / 3.86 ( 2841) link_NAG-ASN : bond 0.00314 / 0.20 ( 13) link_NAG-ASN : angle 1.93153 / 1.29 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5083 (t0) cc_final: 0.4755 (t0) REVERT: A 141 LEU cc_start: 0.6154 (mt) cc_final: 0.5375 (tp) REVERT: A 153 MET cc_start: 0.3139 (tpt) cc_final: 0.2345 (ptp) REVERT: A 400 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7913 (p90) REVERT: A 558 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7829 (ptpt) REVERT: H 6 GLU cc_start: 0.5355 (mm-30) cc_final: 0.5071 (mm-30) REVERT: H 37 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5626 (t80) REVERT: H 45 ARG cc_start: 0.7598 (mmt180) cc_final: 0.7356 (mmt-90) REVERT: H 58 TYR cc_start: 0.7867 (t80) cc_final: 0.7250 (t80) REVERT: H 59 TYR cc_start: 0.7095 (m-80) cc_final: 0.6623 (m-80) REVERT: H 89 VAL cc_start: 0.7343 (t) cc_final: 0.7049 (p) REVERT: H 96 TYR cc_start: 0.7366 (t80) cc_final: 0.7078 (t80) REVERT: H 100 ARG cc_start: 0.7629 (mpp-170) cc_final: 0.7248 (mpp80) REVERT: H 100 PHE cc_start: 0.8119 (p90) cc_final: 0.7835 (p90) REVERT: D 37 TYR cc_start: 0.8108 (m-80) cc_final: 0.7558 (m-80) REVERT: D 47 TRP cc_start: 0.7785 (t60) cc_final: 0.7549 (t60) REVERT: D 71 ARG cc_start: 0.6391 (ptt90) cc_final: 0.6079 (ptt90) REVERT: D 75 LYS cc_start: 0.8224 (mmmt) cc_final: 0.8021 (tptp) REVERT: D 100 PHE cc_start: 0.8080 (m-10) cc_final: 0.7834 (m-10) REVERT: C 81 ASN cc_start: 0.6386 (t0) cc_final: 0.6118 (t0) REVERT: C 117 LEU cc_start: 0.7394 (mp) cc_final: 0.7130 (mt) REVERT: C 131 CYS cc_start: 0.4027 (OUTLIER) cc_final: 0.3160 (m) REVERT: C 140 PHE cc_start: 0.5131 (m-80) cc_final: 0.4698 (m-80) REVERT: C 153 MET cc_start: 0.5775 (mmm) cc_final: 0.4697 (ttt) REVERT: C 157 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: C 190 ARG cc_start: 0.5804 (mtm-85) cc_final: 0.5103 (tpt-90) REVERT: C 266 TYR cc_start: 0.7048 (m-80) cc_final: 0.6768 (m-80) REVERT: C 646 ARG cc_start: 0.7723 (tpt90) cc_final: 0.7041 (tpt90) REVERT: B 102 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6822 (mtm-85) REVERT: B 115 GLN cc_start: 0.7420 (mt0) cc_final: 0.7018 (mm-40) outliers start: 40 outliers final: 26 residues processed: 220 average time/residue: 0.1534 time to fit residues: 54.0275 Evaluate side-chains 192 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 138 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073940 restraints weight = 52667.347| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.16 r_work: 0.2921 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23355 Z= 0.166 Angle : 0.557 12.732 31813 Z= 0.291 Chirality : 0.044 0.264 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.514 36.690 3097 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.25 % Allowed : 7.49 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 2844 helix: 2.95 (0.20), residues: 615 sheet: 0.71 (0.19), residues: 671 loop : -0.63 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.026 0.002 TYR H 100F PHE 0.020 0.001 PHE D 67 TRP 0.013 0.001 TRP A 353 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23305) covalent geometry : angle 0.54796 / 0.29 (31700) SS BOND : bond 0.00607 / 0.36 ( 37) SS BOND : angle 1.62340 / 1.04 ( 74) hydrogen bonds : bond 0.04302 / 2.82 ( 997) hydrogen bonds : angle 5.44222 / 3.82 ( 2841) link_NAG-ASN : bond 0.00361 / 0.24 ( 13) link_NAG-ASN : angle 1.98111 / 1.34 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5037 (t0) cc_final: 0.4702 (t0) REVERT: A 141 LEU cc_start: 0.6144 (mt) cc_final: 0.5327 (tp) REVERT: A 153 MET cc_start: 0.3265 (tpt) cc_final: 0.2335 (ptp) REVERT: A 273 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7503 (mmm-85) REVERT: A 400 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8337 (p90) REVERT: A 558 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7839 (ptpt) REVERT: H 37 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5686 (t80) REVERT: H 89 VAL cc_start: 0.7450 (t) cc_final: 0.7222 (p) REVERT: H 96 TYR cc_start: 0.7352 (t80) cc_final: 0.7070 (t80) REVERT: D 47 TRP cc_start: 0.7884 (t60) cc_final: 0.7611 (t60) REVERT: D 71 ARG cc_start: 0.6301 (ptt90) cc_final: 0.6034 (ptt90) REVERT: D 75 LYS cc_start: 0.8207 (mmmt) cc_final: 0.8000 (tptp) REVERT: D 94 ARG cc_start: 0.7230 (ttp80) cc_final: 0.7026 (ttp-170) REVERT: D 100 PHE cc_start: 0.8107 (m-10) cc_final: 0.7630 (m-10) REVERT: D 102 TYR cc_start: 0.8816 (m-80) cc_final: 0.8441 (m-80) REVERT: C 81 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6148 (t0) REVERT: C 131 CYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3083 (m) REVERT: C 153 MET cc_start: 0.5836 (mmm) cc_final: 0.4778 (ttt) REVERT: C 157 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.5157 (m-80) REVERT: C 190 ARG cc_start: 0.5547 (mtm-85) cc_final: 0.5100 (mtm-85) REVERT: C 646 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7139 (tpt90) REVERT: B 115 GLN cc_start: 0.7387 (mt0) cc_final: 0.7055 (mm-40) outliers start: 57 outliers final: 43 residues processed: 221 average time/residue: 0.1488 time to fit residues: 51.2541 Evaluate side-chains 210 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 270 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 275 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C1074 ASN ** B 239 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 = 0.3725 r_free = 0.3725 target = 0.107598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073804 restraints weight = 52995.537| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.22 r_work: 0.2945 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23355 Z= 0.123 Angle : 0.526 11.551 31813 Z= 0.276 Chirality : 0.043 0.248 3631 Planarity : 0.004 0.062 4102 Dihedral : 4.371 32.759 3097 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.77 % Allowed : 8.47 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2844 helix: 3.18 (0.20), residues: 606 sheet: 0.69 (0.20), residues: 641 loop : -0.63 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.020 0.001 TYR H 100F PHE 0.026 0.001 PHE H 98 TRP 0.014 0.002 TRP D 36 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (23305) covalent geometry : angle 0.51553 / 0.27 (31700) SS BOND : bond 0.00497 / 0.30 ( 37) SS BOND : angle 1.86541 / 1.33 ( 74) hydrogen bonds : bond 0.03943 / 2.57 ( 997) hydrogen bonds : angle 5.29965 / 3.72 ( 2841) link_NAG-ASN : bond 0.00283 / 0.19 ( 13) link_NAG-ASN : angle 1.82788 / 1.22 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5055 (t0) cc_final: 0.4711 (t0) REVERT: A 141 LEU cc_start: 0.6027 (mt) cc_final: 0.5279 (tp) REVERT: A 153 MET cc_start: 0.3232 (tpt) cc_final: 0.2303 (ptp) REVERT: A 269 TYR cc_start: 0.7066 (m-10) cc_final: 0.6853 (m-10) REVERT: A 400 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8466 (p90) REVERT: A 558 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7815 (ptpt) REVERT: A 599 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9009 (p) REVERT: H 37 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5689 (t80) REVERT: H 68 THR cc_start: 0.6418 (t) cc_final: 0.6213 (t) REVERT: H 89 VAL cc_start: 0.7516 (t) cc_final: 0.7264 (p) REVERT: H 96 TYR cc_start: 0.7354 (t80) cc_final: 0.7050 (t80) REVERT: H 100 ARG cc_start: 0.7951 (mpp-170) cc_final: 0.7362 (mpp80) REVERT: H 103 TRP cc_start: 0.6551 (OUTLIER) cc_final: 0.5834 (m-90) REVERT: D 37 TYR cc_start: 0.8060 (m-80) cc_final: 0.7453 (m-80) REVERT: D 47 TRP cc_start: 0.7872 (t60) cc_final: 0.7647 (t60) REVERT: D 71 ARG cc_start: 0.6352 (ptt90) cc_final: 0.6132 (ptt90) REVERT: D 75 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7996 (tptp) REVERT: C 131 CYS cc_start: 0.3824 (OUTLIER) cc_final: 0.3033 (m) REVERT: C 153 MET cc_start: 0.5835 (mmm) cc_final: 0.4765 (ttt) REVERT: C 157 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.5459 (m-80) REVERT: C 646 ARG cc_start: 0.7769 (tpt90) cc_final: 0.7108 (tpt90) REVERT: B 115 GLN cc_start: 0.7399 (mt0) cc_final: 0.7055 (mm-40) outliers start: 45 outliers final: 29 residues processed: 203 average time/residue: 0.1333 time to fit residues: 43.2948 Evaluate side-chains 190 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 175 optimal weight: 8.9990 chunk 269 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 246 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 277 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073899 restraints weight = 53071.265| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.10 r_work: 0.2936 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23355 Z= 0.139 Angle : 0.527 13.340 31813 Z= 0.275 Chirality : 0.043 0.245 3631 Planarity : 0.004 0.055 4102 Dihedral : 4.329 28.268 3097 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 2.01 % Allowed : 8.20 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 2844 helix: 3.02 (0.20), residues: 620 sheet: 0.67 (0.20), residues: 653 loop : -0.60 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.023 0.001 TYR H 59 PHE 0.025 0.001 PHE H 98 TRP 0.020 0.002 TRP B 64 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (23305) covalent geometry : angle 0.51902 / 0.27 (31700) SS BOND : bond 0.00617 / 0.39 ( 37) SS BOND : angle 1.46225 / 1.00 ( 74) hydrogen bonds : bond 0.03973 / 2.59 ( 997) hydrogen bonds : angle 5.25998 / 3.69 ( 2841) link_NAG-ASN : bond 0.00308 / 0.21 ( 13) link_NAG-ASN : angle 1.82349 / 1.22 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5052 (t0) cc_final: 0.4793 (t0) REVERT: A 269 TYR cc_start: 0.7101 (m-10) cc_final: 0.6877 (m-10) REVERT: A 558 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7910 (ptpt) REVERT: A 613 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: H 37 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.5704 (t80) REVERT: H 59 TYR cc_start: 0.7266 (m-80) cc_final: 0.6762 (m-80) REVERT: H 89 VAL cc_start: 0.7501 (t) cc_final: 0.7230 (p) REVERT: H 96 TYR cc_start: 0.7359 (t80) cc_final: 0.7068 (t80) REVERT: H 100 ARG cc_start: 0.8086 (mpp-170) cc_final: 0.7695 (mpp80) REVERT: H 103 TRP cc_start: 0.6589 (OUTLIER) cc_final: 0.5914 (m-90) REVERT: D 37 TYR cc_start: 0.8076 (m-80) cc_final: 0.7455 (m-80) REVERT: D 71 ARG cc_start: 0.6345 (ptt90) cc_final: 0.6136 (ptt90) REVERT: D 75 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8073 (tptp) REVERT: D 78 LEU cc_start: 0.7681 (tp) cc_final: 0.7363 (tp) REVERT: D 100 PHE cc_start: 0.8081 (m-10) cc_final: 0.7814 (m-10) REVERT: D 101 ASP cc_start: 0.7991 (m-30) cc_final: 0.7596 (m-30) REVERT: C 131 CYS cc_start: 0.3815 (OUTLIER) cc_final: 0.3099 (m) REVERT: C 153 MET cc_start: 0.5873 (mmm) cc_final: 0.4786 (ttt) REVERT: C 157 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: C 646 ARG cc_start: 0.7770 (tpt90) cc_final: 0.7107 (tpt90) REVERT: B 115 GLN cc_start: 0.7380 (mt0) cc_final: 0.7056 (mm-40) outliers start: 51 outliers final: 43 residues processed: 203 average time/residue: 0.1319 time to fit residues: 43.7554 Evaluate side-chains 203 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 12 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 250 optimal weight: 0.3980 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN B 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.107097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073564 restraints weight = 52872.343| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.22 r_work: 0.2937 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23355 Z= 0.133 Angle : 0.519 12.929 31813 Z= 0.271 Chirality : 0.043 0.240 3631 Planarity : 0.004 0.057 4102 Dihedral : 4.250 24.589 3095 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 1.93 % Allowed : 8.55 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2844 helix: 3.14 (0.20), residues: 612 sheet: 0.73 (0.20), residues: 638 loop : -0.60 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.019 0.001 TYR H 59 PHE 0.026 0.001 PHE H 98 TRP 0.025 0.002 TRP D 47 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (23305) covalent geometry : angle 0.51265 / 0.27 (31700) SS BOND : bond 0.00544 / 0.32 ( 37) SS BOND : angle 1.30207 / 0.87 ( 74) hydrogen bonds : bond 0.03884 / 2.53 ( 997) hydrogen bonds : angle 5.20679 / 3.65 ( 2841) link_NAG-ASN : bond 0.00288 / 0.19 ( 13) link_NAG-ASN : angle 1.79222 / 1.20 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7855 (ptpt) REVERT: A 599 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8997 (p) REVERT: H 37 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.5839 (t80) REVERT: H 59 TYR cc_start: 0.7046 (m-80) cc_final: 0.6562 (m-80) REVERT: H 89 VAL cc_start: 0.7534 (t) cc_final: 0.7255 (p) REVERT: H 96 TYR cc_start: 0.7337 (t80) cc_final: 0.7005 (t80) REVERT: H 100 ARG cc_start: 0.8107 (mpp-170) cc_final: 0.7718 (mpp80) REVERT: H 103 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.5900 (m-90) REVERT: D 37 TYR cc_start: 0.8069 (m-80) cc_final: 0.7428 (m-80) REVERT: D 71 ARG cc_start: 0.6320 (ptt90) cc_final: 0.5944 (ptt90) REVERT: D 75 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8093 (tptp) REVERT: D 91 TYR cc_start: 0.8068 (m-80) cc_final: 0.7585 (m-80) REVERT: D 100 PHE cc_start: 0.8215 (m-10) cc_final: 0.7983 (m-10) REVERT: D 103 TRP cc_start: 0.7163 (m100) cc_final: 0.6429 (m100) REVERT: C 131 CYS cc_start: 0.3765 (OUTLIER) cc_final: 0.2979 (m) REVERT: C 153 MET cc_start: 0.5859 (mmm) cc_final: 0.4753 (ttt) REVERT: C 646 ARG cc_start: 0.7832 (tpt90) cc_final: 0.7156 (tpt90) REVERT: B 115 GLN cc_start: 0.7394 (mt0) cc_final: 0.7056 (mm-40) outliers start: 49 outliers final: 42 residues processed: 209 average time/residue: 0.1276 time to fit residues: 43.3384 Evaluate side-chains 196 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 252 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 206 optimal weight: 0.0030 chunk 245 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.108308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074801 restraints weight = 53367.998| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.30 r_work: 0.2969 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 23355 Z= 0.100 Angle : 0.498 12.919 31813 Z= 0.261 Chirality : 0.043 0.234 3631 Planarity : 0.004 0.057 4102 Dihedral : 4.093 23.321 3095 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 1.54 % Allowed : 9.02 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2844 helix: 3.22 (0.20), residues: 615 sheet: 0.76 (0.20), residues: 629 loop : -0.58 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.024 0.001 TYR H 100F PHE 0.032 0.001 PHE H 98 TRP 0.040 0.002 TRP D 47 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (23305) covalent geometry : angle 0.49219 / 0.26 (31700) SS BOND : bond 0.00453 / 0.25 ( 37) SS BOND : angle 1.15019 / 0.76 ( 74) hydrogen bonds : bond 0.03549 / 2.32 ( 997) hydrogen bonds : angle 5.02548 / 3.53 ( 2841) link_NAG-ASN : bond 0.00221 / 0.14 ( 13) link_NAG-ASN : angle 1.64663 / 1.08 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5945 (mt) cc_final: 0.5146 (tp) REVERT: A 160 TYR cc_start: 0.4260 (m-80) cc_final: 0.3946 (m-10) REVERT: A 558 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7861 (ptpt) REVERT: A 599 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9020 (p) REVERT: A 613 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: H 37 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.6106 (t80) REVERT: H 59 TYR cc_start: 0.7022 (m-80) cc_final: 0.6578 (m-80) REVERT: H 89 VAL cc_start: 0.7555 (t) cc_final: 0.7250 (p) REVERT: H 96 TYR cc_start: 0.7326 (t80) cc_final: 0.7063 (t80) REVERT: H 100 ARG cc_start: 0.7968 (mpp-170) cc_final: 0.7658 (mpp80) REVERT: H 103 TRP cc_start: 0.6461 (OUTLIER) cc_final: 0.5661 (m-90) REVERT: D 75 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8059 (tptp) REVERT: D 101 ASP cc_start: 0.7786 (m-30) cc_final: 0.7341 (m-30) REVERT: C 153 MET cc_start: 0.5936 (mmm) cc_final: 0.4648 (ttm) REVERT: C 646 ARG cc_start: 0.7846 (tpt90) cc_final: 0.7134 (tpt90) REVERT: B 115 GLN cc_start: 0.7387 (mt0) cc_final: 0.7031 (mm-40) outliers start: 39 outliers final: 28 residues processed: 202 average time/residue: 0.1425 time to fit residues: 46.4242 Evaluate side-chains 181 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 61 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 264 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074433 restraints weight = 53047.918| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.28 r_work: 0.2943 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23355 Z= 0.122 Angle : 0.514 12.662 31813 Z= 0.268 Chirality : 0.043 0.235 3631 Planarity : 0.004 0.056 4102 Dihedral : 4.109 22.854 3095 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 8.94 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2844 helix: 3.22 (0.20), residues: 615 sheet: 0.75 (0.20), residues: 634 loop : -0.58 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 45 TYR 0.026 0.001 TYR H 100F PHE 0.031 0.001 PHE H 98 TRP 0.040 0.002 TRP D 47 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (23305) covalent geometry : angle 0.50843 / 0.27 (31700) SS BOND : bond 0.00496 / 0.29 ( 37) SS BOND : angle 1.18902 / 0.78 ( 74) hydrogen bonds : bond 0.03713 / 2.43 ( 997) hydrogen bonds : angle 5.04955 / 3.55 ( 2841) link_NAG-ASN : bond 0.00268 / 0.18 ( 13) link_NAG-ASN : angle 1.66239 / 1.11 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.4477 (m-80) cc_final: 0.4105 (m-10) REVERT: A 558 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7859 (ptpt) REVERT: A 599 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9006 (p) REVERT: A 613 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: H 37 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.6131 (t80) REVERT: H 59 TYR cc_start: 0.7080 (m-80) cc_final: 0.6623 (m-80) REVERT: H 89 VAL cc_start: 0.7568 (t) cc_final: 0.7251 (p) REVERT: H 96 TYR cc_start: 0.7181 (t80) cc_final: 0.6946 (t80) REVERT: H 100 ARG cc_start: 0.7925 (mpp-170) cc_final: 0.7598 (mpp80) REVERT: H 103 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.5857 (m-90) REVERT: D 75 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7888 (tptp) REVERT: C 117 LEU cc_start: 0.7524 (mp) cc_final: 0.7229 (mt) REVERT: C 131 CYS cc_start: 0.3715 (OUTLIER) cc_final: 0.3017 (m) REVERT: C 153 MET cc_start: 0.5828 (mmm) cc_final: 0.4855 (ttp) REVERT: C 646 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7161 (tpt90) REVERT: B 115 GLN cc_start: 0.7373 (mt0) cc_final: 0.7038 (mm-40) outliers start: 44 outliers final: 33 residues processed: 183 average time/residue: 0.1359 time to fit residues: 40.7069 Evaluate side-chains 176 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 249 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072813 restraints weight = 53063.401| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.07 r_work: 0.2961 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23355 Z= 0.136 Angle : 0.524 12.643 31813 Z= 0.273 Chirality : 0.043 0.244 3631 Planarity : 0.004 0.056 4102 Dihedral : 4.178 24.229 3095 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.65 % Allowed : 8.98 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2844 helix: 3.24 (0.20), residues: 612 sheet: 0.72 (0.20), residues: 633 loop : -0.62 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 45 TYR 0.026 0.001 TYR H 100F PHE 0.030 0.001 PHE H 98 TRP 0.069 0.003 TRP D 47 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (23305) covalent geometry : angle 0.51797 / 0.27 (31700) SS BOND : bond 0.00517 / 0.31 ( 37) SS BOND : angle 1.24032 / 0.82 ( 74) hydrogen bonds : bond 0.03829 / 2.51 ( 997) hydrogen bonds : angle 5.08520 / 3.57 ( 2841) link_NAG-ASN : bond 0.00288 / 0.20 ( 13) link_NAG-ASN : angle 1.70711 / 1.14 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6237.81 seconds wall clock time: 107 minutes 20.46 seconds (6440.46 seconds total)