Starting phenix.real_space_refine on Sun Aug 24 21:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_27692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_27692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_27692.map" model { file = "/net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_27692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dt8_27692/08_2025/8dt8_27692.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 18 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 dihedrals: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.01, per 1000 atoms: 0.22 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.12 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: 5.38 Time building geometry restraints manager: 2.51 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: 13496 17.43 - 34.86: 413 34.86 - 52.28: 94 52.28 - 69.71: 60 69.71 - 87.14: 20 Dihedral angle restraints: 14083 sinusoidal: 5667 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 14080 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 22.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 10.603 87.138 8554 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 aren 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 covalent geometry : bond 0.00550 (23305) covalent geometry : angle 0.97387 (31700) SS BOND : bond 0.02216 ( 37) SS BOND : angle 7.70451 ( 74) hydrogen bonds : bond 0.13236 ( 997) hydrogen bonds : angle 7.63291 ( 2841) link_NAG-ASN : bond 0.00204 ( 13) link_NAG-ASN : angle 2.15956 ( 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 : 0.997 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: 0.1859 time to fit residues: 129.4900 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 : 0.794 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 710 ASN A 955 ASN H 82AASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 532 ASN C 655 HIS C 926 GLN C 935 GLN C 955 ASN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073460 restraints weight = 53034.965| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.28 r_work: 0.2931 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 23355 Z= 0.245 Angle : 0.675 14.152 31813 Z= 0.361 Chirality : 0.048 0.363 3631 Planarity : 0.005 0.040 4102 Dihedral : 5.266 58.957 3374 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.89 % Allowed : 4.96 % Favored : 93.14 % 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 aren not related in a simple way. whole: 0.88 (0.15), residues: 2844 helix: 2.42 (0.20), residues: 607 sheet: 0.98 (0.19), residues: 653 loop : -0.31 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 94 TYR 0.022 0.002 TYR A1067 PHE 0.022 0.002 PHE B 133 TRP 0.016 0.002 TRP A 353 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00583 (23305) covalent geometry : angle 0.66669 (31700) SS BOND : bond 0.00922 ( 37) SS BOND : angle 1.75894 ( 74) hydrogen bonds : bond 0.05297 ( 997) hydrogen bonds : angle 6.07238 ( 2841) link_NAG-ASN : bond 0.00517 ( 13) link_NAG-ASN : angle 2.18770 ( 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 263 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5872 (mt) cc_final: 0.5404 (tp) REVERT: A 153 MET cc_start: 0.2719 (tpt) cc_final: 0.2222 (ptp) REVERT: A 170 TYR cc_start: 0.7276 (t80) cc_final: 0.7057 (t80) REVERT: A 271 GLN cc_start: 0.7841 (mp10) cc_final: 0.7590 (mp10) REVERT: A 558 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7745 (ptpt) REVERT: H 37 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5741 (t80) REVERT: H 45 ARG cc_start: 0.7688 (mmp80) cc_final: 0.7379 (mmt180) REVERT: H 59 TYR cc_start: 0.6548 (m-80) cc_final: 0.6010 (m-80) REVERT: H 96 TYR cc_start: 0.7474 (t80) cc_final: 0.7213 (t80) REVERT: H 100 ARG cc_start: 0.7467 (mpp-170) cc_final: 0.6960 (mpp80) REVERT: D 36 TRP cc_start: 0.7042 (m100) cc_final: 0.6620 (m100) REVERT: D 37 TYR cc_start: 0.8087 (m-80) cc_final: 0.7518 (m-80) REVERT: D 43 LYS cc_start: 0.6894 (mppt) cc_final: 0.6537 (mmtt) REVERT: D 81 GLN cc_start: 0.7372 (tm-30) cc_final: 0.6791 (tm-30) REVERT: D 100 PHE cc_start: 0.8079 (m-10) cc_final: 0.7429 (m-10) REVERT: C 131 CYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3444 (m) REVERT: C 153 MET cc_start: 0.5796 (mmm) cc_final: 0.4578 (ttt) REVERT: C 190 ARG cc_start: 0.5893 (mtm-85) cc_final: 0.5402 (tpp80) REVERT: C 646 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7115 (tpt90) REVERT: B 102 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6989 (mtm-85) REVERT: B 115 GLN cc_start: 0.7405 (mt0) cc_final: 0.7024 (mm-40) REVERT: B 541 PHE cc_start: 0.7101 (p90) cc_final: 0.6837 (p90) outliers start: 48 outliers final: 27 residues processed: 248 average time/residue: 0.1615 time to fit residues: 61.9316 Evaluate side-chains 196 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 117 LEU 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 1050 MET Chi-restraints excluded: chain C residue 1098 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: 1.9990 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: 1.9990 chunk 106 optimal weight: 0.0010 chunk 28 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 73 ASN D 76 ASN C 81 ASN B 165 ASN B 239 GLN B 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.108447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074846 restraints weight = 53145.242| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.25 r_work: 0.2948 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23355 Z= 0.148 Angle : 0.565 9.366 31813 Z= 0.298 Chirality : 0.044 0.249 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.871 50.656 3372 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 7.01 % Favored : 91.45 % 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 aren not related in a simple way. whole: 0.89 (0.15), residues: 2844 helix: 2.96 (0.20), residues: 601 sheet: 0.83 (0.19), residues: 639 loop : -0.45 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 71 TYR 0.024 0.002 TYR H 100F PHE 0.021 0.002 PHE B 133 TRP 0.017 0.001 TRP D 36 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00342 (23305) covalent geometry : angle 0.55749 (31700) SS BOND : bond 0.00600 ( 37) SS BOND : angle 1.48567 ( 74) hydrogen bonds : bond 0.04422 ( 997) hydrogen bonds : angle 5.63712 ( 2841) link_NAG-ASN : bond 0.00338 ( 13) link_NAG-ASN : angle 1.97656 ( 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 227 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5080 (t0) cc_final: 0.4754 (t0) REVERT: A 141 LEU cc_start: 0.6026 (mt) cc_final: 0.5300 (tp) REVERT: A 153 MET cc_start: 0.3029 (tpt) cc_final: 0.2347 (ptp) REVERT: A 168 PHE cc_start: 0.4794 (t80) cc_final: 0.4583 (t80) REVERT: A 558 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7800 (ptpt) REVERT: H 37 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5651 (t80) REVERT: H 46 GLU cc_start: 0.8440 (tp30) cc_final: 0.8185 (tp30) REVERT: H 89 VAL cc_start: 0.7407 (t) cc_final: 0.7133 (p) REVERT: H 96 TYR cc_start: 0.7463 (t80) cc_final: 0.7194 (t80) REVERT: H 100 ARG cc_start: 0.7566 (mpp-170) cc_final: 0.7258 (mpp80) REVERT: D 37 TYR cc_start: 0.8073 (m-80) cc_final: 0.7525 (m-80) REVERT: D 71 ARG cc_start: 0.6198 (ptt90) cc_final: 0.5951 (ptt-90) REVERT: D 82 MET cc_start: 0.7217 (mpp) cc_final: 0.7013 (mpp) REVERT: C 81 ASN cc_start: 0.6594 (t0) cc_final: 0.6307 (t0) REVERT: C 131 CYS cc_start: 0.4292 (OUTLIER) cc_final: 0.3563 (m) REVERT: C 153 MET cc_start: 0.5779 (mmm) cc_final: 0.4633 (ttt) REVERT: C 190 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5074 (tpt-90) REVERT: C 646 ARG cc_start: 0.7708 (tpt90) cc_final: 0.7041 (tpt90) REVERT: B 102 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6899 (mtm-85) REVERT: B 115 GLN cc_start: 0.7521 (mt0) cc_final: 0.7011 (mm-40) REVERT: B 795 LYS cc_start: 0.6318 (mmtm) cc_final: 0.6099 (mmtm) outliers start: 39 outliers final: 24 residues processed: 219 average time/residue: 0.1678 time to fit residues: 57.1529 Evaluate side-chains 186 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL 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 C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU 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 985 ASP Chi-restraints excluded: chain C residue 1098 ASN 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 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: 5.9990 chunk 113 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.0050 chunk 224 optimal weight: 0.2980 chunk 105 optimal weight: 20.0000 chunk 274 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 901 GLN C1074 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075489 restraints weight = 53276.018| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.21 r_work: 0.2960 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23355 Z= 0.127 Angle : 0.530 13.516 31813 Z= 0.279 Chirality : 0.043 0.272 3631 Planarity : 0.004 0.045 4102 Dihedral : 4.620 45.344 3372 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 7.21 % Favored : 91.21 % 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 aren not related in a simple way. whole: 0.94 (0.15), residues: 2844 helix: 3.20 (0.20), residues: 599 sheet: 0.81 (0.19), residues: 662 loop : -0.50 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 71 TYR 0.021 0.001 TYR H 100F PHE 0.024 0.001 PHE C 135 TRP 0.017 0.001 TRP D 36 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00287 (23305) covalent geometry : angle 0.52300 (31700) SS BOND : bond 0.00602 ( 37) SS BOND : angle 1.37754 ( 74) hydrogen bonds : bond 0.04041 ( 997) hydrogen bonds : angle 5.40559 ( 2841) link_NAG-ASN : bond 0.00300 ( 13) link_NAG-ASN : angle 1.85903 ( 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 227 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.4915 (t0) cc_final: 0.4581 (t0) REVERT: A 141 LEU cc_start: 0.6079 (mt) cc_final: 0.5309 (tp) REVERT: A 153 MET cc_start: 0.3050 (tpt) cc_final: 0.2306 (ptp) REVERT: A 400 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7818 (p90) REVERT: A 558 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7840 (ptpt) REVERT: H 37 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.5643 (t80) REVERT: H 45 ARG cc_start: 0.7610 (mmp80) cc_final: 0.7385 (mmt180) REVERT: H 46 GLU cc_start: 0.8550 (tp30) cc_final: 0.8321 (tp30) REVERT: H 58 TYR cc_start: 0.7784 (t80) cc_final: 0.7196 (t80) REVERT: H 59 TYR cc_start: 0.6934 (m-80) cc_final: 0.6442 (m-80) REVERT: H 89 VAL cc_start: 0.7460 (t) cc_final: 0.6939 (p) REVERT: H 96 TYR cc_start: 0.7333 (t80) cc_final: 0.6991 (t80) REVERT: H 100 ARG cc_start: 0.7682 (mpp-170) cc_final: 0.7479 (mpp80) REVERT: D 37 TYR cc_start: 0.8089 (m-80) cc_final: 0.7458 (m-80) REVERT: D 71 ARG cc_start: 0.6394 (ptt90) cc_final: 0.6053 (ptt90) REVERT: D 82 MET cc_start: 0.7371 (mpp) cc_final: 0.6980 (mpp) REVERT: C 81 ASN cc_start: 0.6521 (t0) cc_final: 0.6217 (t0) REVERT: C 131 CYS cc_start: 0.4205 (OUTLIER) cc_final: 0.3557 (m) REVERT: C 153 MET cc_start: 0.5774 (mmm) cc_final: 0.4668 (ttt) REVERT: C 190 ARG cc_start: 0.5830 (mtm-85) cc_final: 0.5074 (tpt-90) REVERT: C 646 ARG cc_start: 0.7744 (tpt90) cc_final: 0.7046 (tpt90) REVERT: B 102 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6934 (mtm-85) REVERT: B 115 GLN cc_start: 0.7449 (mt0) cc_final: 0.7020 (mm-40) REVERT: B 795 LYS cc_start: 0.6231 (mmtm) cc_final: 0.6006 (mmtm) outliers start: 40 outliers final: 24 residues processed: 216 average time/residue: 0.1702 time to fit residues: 57.9801 Evaluate side-chains 181 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL 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 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 H residue 48 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain C residue 117 LEU 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 588 THR Chi-restraints excluded: chain C residue 985 ASP 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 138 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN B 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.108092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074583 restraints weight = 52884.603| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.29 r_work: 0.2944 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23355 Z= 0.135 Angle : 0.527 12.928 31813 Z= 0.275 Chirality : 0.043 0.256 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.442 39.709 3370 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 1.65 % Allowed : 7.80 % Favored : 90.54 % 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 aren not related in a simple way. whole: 0.92 (0.15), residues: 2844 helix: 3.24 (0.20), residues: 600 sheet: 0.82 (0.19), residues: 651 loop : -0.54 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.025 0.001 TYR H 100F PHE 0.019 0.001 PHE C 135 TRP 0.013 0.002 TRP D 36 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00313 (23305) covalent geometry : angle 0.51940 (31700) SS BOND : bond 0.00584 ( 37) SS BOND : angle 1.36812 ( 74) hydrogen bonds : bond 0.04007 ( 997) hydrogen bonds : angle 5.30492 ( 2841) link_NAG-ASN : bond 0.00298 ( 13) link_NAG-ASN : angle 1.82661 ( 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 227 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5037 (t0) cc_final: 0.4713 (t0) REVERT: A 141 LEU cc_start: 0.6076 (mt) cc_final: 0.5258 (tp) REVERT: A 153 MET cc_start: 0.3101 (tpt) cc_final: 0.2312 (ptp) REVERT: A 273 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7385 (mmm-85) REVERT: A 400 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8173 (p90) REVERT: A 558 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7827 (ptpt) REVERT: H 37 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5690 (t80) REVERT: H 46 GLU cc_start: 0.8482 (tp30) cc_final: 0.8242 (tp30) REVERT: H 58 TYR cc_start: 0.7782 (t80) cc_final: 0.7248 (t80) REVERT: H 59 TYR cc_start: 0.6949 (m-80) cc_final: 0.6399 (m-80) REVERT: H 89 VAL cc_start: 0.7423 (t) cc_final: 0.7145 (p) REVERT: H 96 TYR cc_start: 0.7315 (t80) cc_final: 0.7009 (t80) REVERT: D 37 TYR cc_start: 0.8091 (m-80) cc_final: 0.7512 (m-80) REVERT: D 71 ARG cc_start: 0.6349 (ptt90) cc_final: 0.5999 (ptt90) REVERT: D 75 LYS cc_start: 0.8228 (mmmt) cc_final: 0.8009 (tptp) REVERT: D 82 MET cc_start: 0.7270 (mpp) cc_final: 0.7067 (mpp) REVERT: D 103 TRP cc_start: 0.7469 (m100) cc_final: 0.6190 (m100) REVERT: C 81 ASN cc_start: 0.6377 (t0) cc_final: 0.6144 (t0) REVERT: C 131 CYS cc_start: 0.4170 (OUTLIER) cc_final: 0.3545 (m) REVERT: C 153 MET cc_start: 0.5725 (mmm) cc_final: 0.4620 (ttt) REVERT: C 190 ARG cc_start: 0.5624 (mtm-85) cc_final: 0.5308 (mtm-85) REVERT: C 646 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7070 (tpt90) REVERT: B 102 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6864 (mtm-85) REVERT: B 115 GLN cc_start: 0.7420 (mt0) cc_final: 0.7056 (mm-40) outliers start: 42 outliers final: 31 residues processed: 218 average time/residue: 0.1674 time to fit residues: 58.0128 Evaluate side-chains 195 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL 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 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 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 C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU 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 588 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 602 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2601 > 50: distance: 100 - 166: 31.250 distance: 114 - 153: 34.629 distance: 117 - 150: 31.788 distance: 133 - 137: 23.166 distance: 137 - 138: 31.632 distance: 138 - 141: 3.708 distance: 139 - 140: 6.222 distance: 139 - 142: 27.911 distance: 142 - 143: 5.818 distance: 143 - 144: 4.237 distance: 143 - 146: 40.687 distance: 144 - 145: 41.529 distance: 146 - 147: 40.112 distance: 147 - 148: 8.453 distance: 147 - 149: 20.290 distance: 150 - 151: 17.851 distance: 151 - 152: 33.841 distance: 151 - 154: 21.347 distance: 152 - 153: 43.331 distance: 152 - 159: 18.294 distance: 154 - 155: 16.396 distance: 155 - 156: 48.731 distance: 156 - 157: 28.085 distance: 156 - 158: 17.516 distance: 159 - 160: 20.544 distance: 159 - 165: 13.921 distance: 160 - 161: 34.306 distance: 160 - 163: 11.955 distance: 161 - 162: 6.261 distance: 161 - 166: 19.817 distance: 163 - 164: 42.230 distance: 164 - 165: 28.224 distance: 166 - 167: 35.840 distance: 167 - 168: 37.705 distance: 167 - 170: 28.524 distance: 168 - 169: 9.998 distance: 168 - 174: 19.585 distance: 170 - 171: 15.746 distance: 171 - 172: 22.496 distance: 171 - 173: 3.593 distance: 174 - 175: 32.376 distance: 175 - 176: 30.356 distance: 175 - 178: 10.518 distance: 176 - 177: 35.306 distance: 176 - 181: 27.269 distance: 178 - 179: 15.461 distance: 178 - 180: 27.052 distance: 181 - 182: 29.525 distance: 182 - 183: 28.708 distance: 182 - 185: 13.234 distance: 183 - 184: 12.119 distance: 183 - 189: 12.665 distance: 185 - 186: 6.320 distance: 186 - 187: 13.916 distance: 186 - 188: 9.054 distance: 189 - 190: 51.370 distance: 190 - 193: 25.584 distance: 191 - 192: 40.904 distance: 194 - 195: 12.007 distance: 194 - 196: 41.016 distance: 197 - 198: 26.549 distance: 198 - 199: 25.951 distance: 198 - 201: 21.274 distance: 199 - 200: 31.919 distance: 199 - 204: 6.314 distance: 201 - 202: 40.882 distance: 202 - 203: 38.311 distance: 204 - 205: 11.299 distance: 205 - 206: 12.463 distance: 206 - 207: 17.520 distance: 206 - 212: 23.452 distance: 208 - 209: 17.901 distance: 208 - 210: 24.078 distance: 209 - 211: 39.504