Starting phenix.real_space_refine on Sun Aug 24 13:25:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.map" model { file = "/net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d55_46574/08_2025/9d55_46574.cif" } resolution = 3.15 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= 0.014 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 86 5.16 5 C 12802 2.51 5 N 3373 2.21 5 O 3755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s 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: 20016 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 9783 Classifications: {'peptide': 1201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 72, 'TRANS': 1128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9773 Classifications: {'peptide': 1199} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1126} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.01, per 1000 atoms: 0.25 Number of scatterers: 20016 At special positions: 0 Unit cell: (108.206, 137.942, 158.592, 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 86 16.00 O 3755 8.00 N 3373 7.00 C 12802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.04 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 528 " distance=2.02 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 734 " distance=2.02 Simple disulfide: pdb=" SG CYS B 928 " - pdb=" SG CYS B 946 " distance=2.03 Simple disulfide: pdb=" SG CYS B1114 " - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 82 " " NAG A1302 " - " ASN A 648 " " NAG A1303 " - " ASN A 666 " " NAG B1301 " - " ASN B 9 " " NAG B1302 " - " ASN B 666 " " NAG D 1 " - " ASN A 25 " " NAG F 1 " - " ASN A 117 " " NAG G 1 " - " ASN A 289 " " NAG H 1 " - " ASN A 416 " " NAG I 1 " - " ASN A 480 " " NAG L 1 " - " ASN A 685 " " NAG N 1 " - " ASN B 25 " " NAG P 1 " - " ASN B 117 " " NAG Q 1 " - " ASN B 289 " " NAG R 1 " - " ASN B 416 " " NAG S 1 " - " ASN B 480 " " NAG U 1 " - " ASN B 685 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 830.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 7 sheets defined 66.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.843A pdb=" N ALA A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.903A pdb=" N ARG A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.714A pdb=" N ALA A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 171 through 190 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 261 through 268 removed outlier: 4.626A pdb=" N ASP A 266 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 268 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.617A pdb=" N MET A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 304 removed outlier: 4.102A pdb=" N ALA A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.722A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 372 Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.703A pdb=" N ALA A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 435 through 451 removed outlier: 4.332A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 498 through 519 removed outlier: 4.095A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.511A pdb=" N ALA A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 removed outlier: 3.522A pdb=" N VAL A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 616 through 648 removed outlier: 4.096A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.728A pdb=" N SER A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.331A pdb=" N ASP A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.789A pdb=" N ALA A 702 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 724 Processing helix chain 'A' and resid 740 through 748 Processing helix chain 'A' and resid 750 through 770 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 804 through 836 Proline residue: A 818 - end of helix Processing helix chain 'A' and resid 887 through 903 removed outlier: 3.563A pdb=" N GLY A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.320A pdb=" N ASN A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.087A pdb=" N TYR A 970 " --> pdb=" O TYR A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 982 through 998 removed outlier: 3.555A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.629A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 4.109A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1068 removed outlier: 3.595A pdb=" N GLU A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A1061 " --> pdb=" O TYR A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1088 through 1093 Processing helix chain 'A' and resid 1096 through 1116 removed outlier: 3.953A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.520A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1158 removed outlier: 3.648A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'A' and resid 1172 through 1187 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 13 through 42 removed outlier: 4.714A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 76 through 83 Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.533A pdb=" N THR B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.020A pdb=" N ASN B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 171 through 190 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.664A pdb=" N TRP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 218 through 238 removed outlier: 3.667A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 291 through 304 removed outlier: 3.796A pdb=" N LEU B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 352 through 372 removed outlier: 3.985A pdb=" N TYR B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.479A pdb=" N ARG B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 400 removed outlier: 3.922A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 417 through 429 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.268A pdb=" N TYR B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.599A pdb=" N ALA B 488 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 489 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 520 removed outlier: 4.141A pdb=" N PHE B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 546 removed outlier: 4.451A pdb=" N ALA B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 616 through 647 removed outlier: 3.922A pdb=" N VAL B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.872A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 704 through 724 Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 750 through 770 Processing helix chain 'B' and resid 772 through 788 Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 804 through 836 Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.547A pdb=" N ASP B 864 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 882 removed outlier: 3.592A pdb=" N ALA B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 885 No H-bonds generated for 'chain 'B' and resid 883 through 885' Processing helix chain 'B' and resid 887 through 903 removed outlier: 3.902A pdb=" N ALA B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 896 " --> pdb=" O PHE B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.692A pdb=" N LEU B 954 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 970 " --> pdb=" O TYR B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 998 removed outlier: 3.799A pdb=" N LEU B 993 " --> pdb=" O ILE B 989 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 996 " --> pdb=" O VAL B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1005 Processing helix chain 'B' and resid 1015 through 1031 removed outlier: 3.522A pdb=" N ASP B1019 " --> pdb=" O SER B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1049 removed outlier: 4.174A pdb=" N ASP B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B1042 " --> pdb=" O TYR B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1068 Processing helix chain 'B' and resid 1082 through 1087 Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.760A pdb=" N SER B1092 " --> pdb=" O HIS B1089 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B1093 " --> pdb=" O ILE B1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1089 through 1093' Processing helix chain 'B' and resid 1096 through 1118 removed outlier: 4.025A pdb=" N PHE B1100 " --> pdb=" O TYR B1096 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE B1107 " --> pdb=" O PHE B1103 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1126 Processing helix chain 'B' and resid 1131 through 1143 Processing helix chain 'B' and resid 1144 through 1148 removed outlier: 3.508A pdb=" N SER B1147 " --> pdb=" O LEU B1144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG B1148 " --> pdb=" O GLY B1145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1144 through 1148' Processing helix chain 'B' and resid 1149 through 1158 removed outlier: 3.737A pdb=" N ALA B1153 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1172 Processing helix chain 'B' and resid 1172 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 5.837A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.409A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.214A pdb=" N ILE B 248 " --> pdb=" O CYS B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.615A pdb=" N VAL B 727 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 735 " --> pdb=" O VAL B 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 846 through 847 removed outlier: 6.544A pdb=" N ILE B 846 " --> pdb=" O CYS B1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 930 through 934 removed outlier: 3.521A pdb=" N SER B 931 " --> pdb=" O LYS B 944 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3099 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: 3.81 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6358 1.34 - 1.46: 4407 1.46 - 1.58: 9707 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20616 Sorted by residual: bond pdb=" C ILE A1090 " pdb=" N PRO A1091 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.39e+00 bond pdb=" CB GLU A 305 " pdb=" CG GLU A 305 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CA ILE B1034 " pdb=" CB ILE B1034 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.09e+00 bond pdb=" C1 NAG Q 2 " pdb=" C2 NAG Q 2 " ideal model delta sigma weight residual 1.532 1.560 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" CA VAL B 495 " pdb=" CB VAL B 495 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.20e-02 6.94e+03 1.61e+00 ... (remaining 20611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 27505 1.94 - 3.89: 472 3.89 - 5.83: 79 5.83 - 7.77: 13 7.77 - 9.72: 6 Bond angle restraints: 28075 Sorted by residual: angle pdb=" N ASP A 374 " pdb=" CA ASP A 374 " pdb=" C ASP A 374 " ideal model delta sigma weight residual 114.62 109.02 5.60 1.14e+00 7.69e-01 2.41e+01 angle pdb=" CA GLU A 305 " pdb=" CB GLU A 305 " pdb=" CG GLU A 305 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" C THR B 84 " pdb=" N ASP B 85 " pdb=" CA ASP B 85 " ideal model delta sigma weight residual 120.68 114.65 6.03 1.52e+00 4.33e-01 1.57e+01 angle pdb=" C TRP B 594 " pdb=" CA TRP B 594 " pdb=" CB TRP B 594 " ideal model delta sigma weight residual 111.00 107.58 3.42 8.70e-01 1.32e+00 1.55e+01 angle pdb=" CA ASP A 374 " pdb=" C ASP A 374 " pdb=" N LEU A 375 " ideal model delta sigma weight residual 119.71 115.82 3.89 1.17e+00 7.31e-01 1.11e+01 ... (remaining 28070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10691 17.96 - 35.91: 1402 35.91 - 53.87: 393 53.87 - 71.82: 86 71.82 - 89.78: 29 Dihedral angle restraints: 12601 sinusoidal: 5547 harmonic: 7054 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -9.71 -76.29 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 516 " pdb=" SG CYS B 516 " pdb=" SG CYS B 528 " pdb=" CB CYS B 528 " ideal model delta sinusoidal sigma weight residual -86.00 -150.72 64.72 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS B1114 " pdb=" SG CYS B1114 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.28 60.28 1 1.00e+01 1.00e-02 4.84e+01 ... (remaining 12598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2749 0.071 - 0.141: 260 0.141 - 0.212: 9 0.212 - 0.282: 1 0.282 - 0.353: 1 Chirality restraints: 3020 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 25 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 117 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3017 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 64 " 0.011 2.00e-02 2.50e+03 1.66e-02 4.81e+00 pdb=" CG PHE A 64 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 64 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 64 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 643 " 0.013 2.00e-02 2.50e+03 1.24e-02 3.85e+00 pdb=" CG TRP A 643 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 643 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 643 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 643 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 643 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 643 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 643 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 305 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C GLU A 305 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU A 305 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 306 " -0.010 2.00e-02 2.50e+03 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2019 2.74 - 3.28: 20438 3.28 - 3.82: 35184 3.82 - 4.36: 39091 4.36 - 4.90: 68156 Nonbonded interactions: 164888 Sorted by model distance: nonbonded pdb=" OE1 GLU A 161 " pdb=" OH TYR A 607 " model vdw 2.203 3.040 nonbonded pdb=" O PHE B 300 " pdb=" OG SER B 303 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU A 212 " pdb=" OH TYR A 440 " model vdw 2.224 3.040 nonbonded pdb=" OG SER A 307 " pdb=" OE1 GLN A 371 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR B 936 " pdb=" O LYS B 971 " model vdw 2.249 3.040 ... (remaining 164883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 1200 or resid 1302 through 1303)) selection = (chain 'B' and (resid 2 through 873 or (resid 874 and (name N or name CA or name \ C or name O or name CB )) or resid 875 through 1302)) } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } 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: 5.330 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.470 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.044 20661 Z= 0.150 Angle : 0.671 19.729 28199 Z= 0.333 Chirality : 0.041 0.353 3020 Planarity : 0.004 0.044 3601 Dihedral : 17.606 89.779 8024 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.66 % Allowed : 25.79 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.18), residues: 2396 helix: 1.18 (0.14), residues: 1499 sheet: None (None), residues: 0 loop : -1.98 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 53 TYR 0.019 0.001 TYR B 24 PHE 0.037 0.001 PHE A 64 TRP 0.034 0.001 TRP A 643 HIS 0.010 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00327 (20616) covalent geometry : angle 0.63195 (28075) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.69707 ( 22) hydrogen bonds : bond 0.12787 ( 1063) hydrogen bonds : angle 5.12738 ( 3099) link_BETA1-4 : bond 0.00759 ( 16) link_BETA1-4 : angle 2.87585 ( 48) link_BETA1-6 : bond 0.00197 ( 1) link_BETA1-6 : angle 1.24502 ( 3) link_NAG-ASN : bond 0.00883 ( 17) link_NAG-ASN : angle 4.43249 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6691 (m-80) cc_final: 0.6195 (m-80) REVERT: A 66 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 155 MET cc_start: 0.8559 (tpp) cc_final: 0.8280 (tpp) REVERT: A 318 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6389 (pp-130) REVERT: A 387 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 403 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 759 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7596 (tt0) REVERT: A 859 TRP cc_start: 0.8531 (OUTLIER) cc_final: 0.7468 (p90) REVERT: A 878 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.6400 (p) REVERT: A 881 MET cc_start: 0.5932 (pmm) cc_final: 0.4175 (mtp) REVERT: A 890 ARG cc_start: 0.7249 (ptm160) cc_final: 0.6923 (ptm160) REVERT: A 1044 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7167 (ttm-80) REVERT: B 40 TRP cc_start: 0.5923 (t60) cc_final: 0.5293 (t60) REVERT: B 343 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: B 625 GLU cc_start: 0.7613 (tp30) cc_final: 0.7155 (mm-30) REVERT: B 662 MET cc_start: 0.5903 (tpt) cc_final: 0.5684 (ttp) REVERT: B 916 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5843 (ptp) REVERT: B 943 ILE cc_start: 0.4143 (pt) cc_final: 0.3815 (pt) REVERT: B 961 MET cc_start: 0.8081 (tpp) cc_final: 0.7761 (tpp) REVERT: B 965 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 979 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6761 (mt-10) REVERT: B 1096 TYR cc_start: 0.8991 (t80) cc_final: 0.8498 (t80) outliers start: 76 outliers final: 63 residues processed: 259 average time/residue: 0.1391 time to fit residues: 56.5166 Evaluate side-chains 263 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 899 PHE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain B residue 1001 LYS Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1154 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 54 GLN B 331 HIS B 404 HIS B 483 HIS B 568 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111683 restraints weight = 29581.607| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.16 r_work: 0.3223 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20661 Z= 0.138 Angle : 0.636 19.887 28199 Z= 0.304 Chirality : 0.041 0.343 3020 Planarity : 0.004 0.049 3601 Dihedral : 8.713 72.255 3459 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.67 % Allowed : 23.87 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.25 (0.18), residues: 2396 helix: 1.31 (0.14), residues: 1506 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 344 TYR 0.017 0.001 TYR A 372 PHE 0.015 0.001 PHE B 33 TRP 0.022 0.001 TRP A 859 HIS 0.011 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00304 (20616) covalent geometry : angle 0.59649 (28075) SS BOND : bond 0.00286 ( 11) SS BOND : angle 1.23621 ( 22) hydrogen bonds : bond 0.04471 ( 1063) hydrogen bonds : angle 4.26651 ( 3099) link_BETA1-4 : bond 0.00778 ( 16) link_BETA1-4 : angle 2.87699 ( 48) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.22533 ( 3) link_NAG-ASN : bond 0.00786 ( 17) link_NAG-ASN : angle 4.41085 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 205 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6669 (m-80) cc_final: 0.6289 (m-80) REVERT: A 155 MET cc_start: 0.8544 (tpp) cc_final: 0.8240 (tpp) REVERT: A 262 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: A 318 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6141 (pp-130) REVERT: A 387 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 403 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 559 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7991 (tpp) REVERT: A 881 MET cc_start: 0.6265 (pmm) cc_final: 0.4359 (mtp) REVERT: A 890 ARG cc_start: 0.7214 (ptm160) cc_final: 0.7009 (ptm160) REVERT: B 33 PHE cc_start: 0.7812 (t80) cc_final: 0.7579 (t80) REVERT: B 40 TRP cc_start: 0.5677 (t60) cc_final: 0.5067 (t60) REVERT: B 295 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7966 (mmt-90) REVERT: B 343 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: B 625 GLU cc_start: 0.7541 (tp30) cc_final: 0.7094 (mm-30) REVERT: B 961 MET cc_start: 0.7990 (tpp) cc_final: 0.7631 (tpp) REVERT: B 965 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6662 (tm-30) REVERT: B 979 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6654 (mt-10) REVERT: B 1096 TYR cc_start: 0.8909 (t80) cc_final: 0.8330 (t80) REVERT: B 1124 HIS cc_start: 0.8279 (p90) cc_final: 0.8044 (p-80) outliers start: 97 outliers final: 57 residues processed: 288 average time/residue: 0.1542 time to fit residues: 69.8599 Evaluate side-chains 260 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1129 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 54 GLN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109833 restraints weight = 29792.405| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.97 r_work: 0.3231 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20661 Z= 0.150 Angle : 0.635 19.848 28199 Z= 0.302 Chirality : 0.042 0.347 3020 Planarity : 0.004 0.053 3601 Dihedral : 7.902 68.568 3393 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.25 % Allowed : 23.00 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.18), residues: 2396 helix: 1.36 (0.14), residues: 1506 sheet: None (None), residues: 0 loop : -1.93 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 942 TYR 0.018 0.001 TYR A 372 PHE 0.013 0.001 PHE A 178 TRP 0.021 0.001 TRP A 859 HIS 0.011 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00344 (20616) covalent geometry : angle 0.59442 (28075) SS BOND : bond 0.00345 ( 11) SS BOND : angle 1.51563 ( 22) hydrogen bonds : bond 0.04337 ( 1063) hydrogen bonds : angle 4.14571 ( 3099) link_BETA1-4 : bond 0.00778 ( 16) link_BETA1-4 : angle 2.87552 ( 48) link_BETA1-6 : bond 0.00229 ( 1) link_BETA1-6 : angle 1.26135 ( 3) link_NAG-ASN : bond 0.00796 ( 17) link_NAG-ASN : angle 4.40062 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 214 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6776 (m-80) cc_final: 0.6362 (m-80) REVERT: A 161 GLU cc_start: 0.8517 (tt0) cc_final: 0.7870 (pt0) REVERT: A 262 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: A 309 MET cc_start: 0.6011 (pmm) cc_final: 0.5739 (pmm) REVERT: A 318 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5919 (pp-130) REVERT: A 387 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 403 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 559 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: A 859 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.7356 (p90) REVERT: A 881 MET cc_start: 0.6506 (pmm) cc_final: 0.4723 (mtp) REVERT: A 1042 GLN cc_start: 0.7825 (tp40) cc_final: 0.7311 (tp40) REVERT: A 1044 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.6825 (ttm-80) REVERT: A 1049 ASP cc_start: 0.8057 (m-30) cc_final: 0.7562 (t0) REVERT: A 1148 ARG cc_start: 0.8271 (mmp80) cc_final: 0.7799 (tpp80) REVERT: B 40 TRP cc_start: 0.5779 (t60) cc_final: 0.5172 (t60) REVERT: B 46 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.4990 (tp) REVERT: B 295 ARG cc_start: 0.8382 (mtt90) cc_final: 0.8039 (mmt-90) REVERT: B 343 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: B 430 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 526 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7517 (m-70) REVERT: B 625 GLU cc_start: 0.7601 (tp30) cc_final: 0.7161 (mm-30) REVERT: B 916 MET cc_start: 0.5814 (mtm) cc_final: 0.5602 (ptp) REVERT: B 961 MET cc_start: 0.8083 (tpp) cc_final: 0.7671 (tpp) REVERT: B 965 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6761 (tm-30) REVERT: B 979 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6675 (mt-10) REVERT: B 1096 TYR cc_start: 0.8947 (t80) cc_final: 0.8435 (t80) REVERT: B 1129 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6599 (m-80) outliers start: 109 outliers final: 68 residues processed: 303 average time/residue: 0.1462 time to fit residues: 69.1485 Evaluate side-chains 278 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 899 PHE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 941 PHE Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1142 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 193 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 108 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 54 GLN B 339 ASN B 404 HIS ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112801 restraints weight = 29635.644| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.89 r_work: 0.3255 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20661 Z= 0.122 Angle : 0.616 19.733 28199 Z= 0.292 Chirality : 0.041 0.354 3020 Planarity : 0.004 0.054 3601 Dihedral : 7.727 63.498 3391 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.10 % Allowed : 23.24 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2396 helix: 1.42 (0.13), residues: 1507 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 942 TYR 0.019 0.001 TYR A 372 PHE 0.013 0.001 PHE A 178 TRP 0.019 0.001 TRP A 859 HIS 0.011 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00264 (20616) covalent geometry : angle 0.57423 (28075) SS BOND : bond 0.00766 ( 11) SS BOND : angle 1.94838 ( 22) hydrogen bonds : bond 0.03906 ( 1063) hydrogen bonds : angle 4.02809 ( 3099) link_BETA1-4 : bond 0.00768 ( 16) link_BETA1-4 : angle 2.86988 ( 48) link_BETA1-6 : bond 0.00287 ( 1) link_BETA1-6 : angle 1.23017 ( 3) link_NAG-ASN : bond 0.00835 ( 17) link_NAG-ASN : angle 4.31291 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 209 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6686 (m-80) cc_final: 0.6250 (m-80) REVERT: A 155 MET cc_start: 0.8472 (tpp) cc_final: 0.8130 (tpp) REVERT: A 262 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: A 309 MET cc_start: 0.5870 (pmm) cc_final: 0.5603 (pmm) REVERT: A 318 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5928 (pp-130) REVERT: A 387 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 403 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 559 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7953 (tpp) REVERT: A 745 MET cc_start: 0.8112 (tpp) cc_final: 0.7876 (ttp) REVERT: A 807 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (mm110) REVERT: A 859 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.7214 (p90) REVERT: A 881 MET cc_start: 0.6526 (pmm) cc_final: 0.4676 (mtp) REVERT: A 1042 GLN cc_start: 0.7668 (tp40) cc_final: 0.7109 (tp40) REVERT: A 1049 ASP cc_start: 0.7976 (m-30) cc_final: 0.7448 (t0) REVERT: A 1148 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7661 (tpp80) REVERT: B 40 TRP cc_start: 0.5903 (t60) cc_final: 0.5282 (t60) REVERT: B 46 ILE cc_start: 0.5704 (OUTLIER) cc_final: 0.4908 (tp) REVERT: B 228 PHE cc_start: 0.8655 (t80) cc_final: 0.8322 (t80) REVERT: B 295 ARG cc_start: 0.8414 (mtt90) cc_final: 0.8007 (mmt-90) REVERT: B 343 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: B 345 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6189 (mt) REVERT: B 526 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7510 (m-70) REVERT: B 625 GLU cc_start: 0.7491 (tp30) cc_final: 0.7054 (mm-30) REVERT: B 638 TYR cc_start: 0.5681 (t80) cc_final: 0.5331 (t80) REVERT: B 916 MET cc_start: 0.5752 (mtm) cc_final: 0.5464 (ptp) REVERT: B 961 MET cc_start: 0.7918 (tpp) cc_final: 0.7516 (tpp) REVERT: B 965 GLN cc_start: 0.6754 (tm-30) cc_final: 0.6549 (tm-30) REVERT: B 979 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6498 (mt-10) REVERT: B 1096 TYR cc_start: 0.8861 (t80) cc_final: 0.8269 (t80) outliers start: 106 outliers final: 69 residues processed: 294 average time/residue: 0.1524 time to fit residues: 70.2718 Evaluate side-chains 274 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 195 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1129 TYR Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 941 PHE Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain B residue 986 HIS Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1142 MET Chi-restraints excluded: chain B residue 1186 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 220 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 42 HIS ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.161206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111653 restraints weight = 29559.090| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.16 r_work: 0.3232 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20661 Z= 0.133 Angle : 0.623 19.727 28199 Z= 0.296 Chirality : 0.041 0.468 3020 Planarity : 0.004 0.054 3601 Dihedral : 7.608 59.948 3389 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.39 % Allowed : 23.15 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2396 helix: 1.48 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : -1.89 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 942 TYR 0.019 0.001 TYR A 372 PHE 0.018 0.001 PHE B 64 TRP 0.020 0.001 TRP A 859 HIS 0.011 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00300 (20616) covalent geometry : angle 0.58364 (28075) SS BOND : bond 0.00504 ( 11) SS BOND : angle 1.64714 ( 22) hydrogen bonds : bond 0.03957 ( 1063) hydrogen bonds : angle 3.99999 ( 3099) link_BETA1-4 : bond 0.00765 ( 16) link_BETA1-4 : angle 2.88059 ( 48) link_BETA1-6 : bond 0.00257 ( 1) link_BETA1-6 : angle 1.24739 ( 3) link_NAG-ASN : bond 0.01275 ( 17) link_NAG-ASN : angle 4.25357 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 207 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 PHE cc_start: 0.6784 (m-80) cc_final: 0.6362 (m-80) REVERT: A 155 MET cc_start: 0.8564 (tpp) cc_final: 0.8291 (tpp) REVERT: A 262 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: A 309 MET cc_start: 0.5927 (pmm) cc_final: 0.5683 (pmm) REVERT: A 387 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 403 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 559 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: A 807 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7476 (mm110) REVERT: A 859 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7346 (p90) REVERT: A 881 MET cc_start: 0.6440 (pmm) cc_final: 0.4774 (mtp) REVERT: A 1042 GLN cc_start: 0.7828 (tp40) cc_final: 0.7328 (tp40) REVERT: A 1044 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.6813 (ttm-80) REVERT: A 1049 ASP cc_start: 0.8053 (m-30) cc_final: 0.7588 (t0) REVERT: A 1148 ARG cc_start: 0.8223 (mmp80) cc_final: 0.7739 (tpp80) REVERT: B 203 ASN cc_start: 0.8107 (t0) cc_final: 0.7878 (t0) REVERT: B 228 PHE cc_start: 0.8779 (t80) cc_final: 0.8448 (t80) REVERT: B 295 ARG cc_start: 0.8404 (mtt90) cc_final: 0.8043 (mmt-90) REVERT: B 343 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 430 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 521 TYR cc_start: 0.7026 (t80) cc_final: 0.6537 (t80) REVERT: B 526 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7569 (m-70) REVERT: B 550 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7423 (mtm110) REVERT: B 625 GLU cc_start: 0.7605 (tp30) cc_final: 0.7163 (mm-30) REVERT: B 638 TYR cc_start: 0.5871 (t80) cc_final: 0.5577 (t80) REVERT: B 916 MET cc_start: 0.5784 (mtm) cc_final: 0.5470 (ptp) REVERT: B 965 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6785 (tm-30) REVERT: B 979 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6648 (mt-10) REVERT: B 1096 TYR cc_start: 0.8924 (t80) cc_final: 0.8396 (t80) outliers start: 112 outliers final: 76 residues processed: 298 average time/residue: 0.1516 time to fit residues: 71.5300 Evaluate side-chains 282 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1129 TYR Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 941 PHE Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain B residue 986 HIS Chi-restraints excluded: chain B residue 1016 ASP Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1142 MET Chi-restraints excluded: chain B residue 1186 HIS Chi-restraints excluded: chain B residue 1198 THR 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: 64.7398 > 50: distance: 14 - 87: 20.536 distance: 17 - 84: 26.057 distance: 26 - 83: 10.016 distance: 37 - 42: 34.801 distance: 42 - 43: 47.020 distance: 43 - 44: 33.847 distance: 43 - 46: 35.761 distance: 44 - 45: 19.968 distance: 44 - 50: 20.601 distance: 46 - 47: 28.819 distance: 47 - 48: 18.227 distance: 47 - 49: 21.607 distance: 50 - 51: 9.869 distance: 51 - 52: 16.389 distance: 51 - 54: 10.184 distance: 52 - 53: 8.442 distance: 52 - 59: 14.043 distance: 54 - 55: 11.520 distance: 55 - 56: 21.466 distance: 56 - 57: 15.431 distance: 57 - 58: 8.120 distance: 59 - 60: 13.776 distance: 60 - 61: 7.667 distance: 60 - 63: 18.731 distance: 61 - 62: 24.039 distance: 61 - 66: 15.128 distance: 63 - 64: 14.301 distance: 63 - 65: 26.896 distance: 66 - 67: 23.162 distance: 67 - 68: 18.711 distance: 67 - 70: 5.229 distance: 68 - 69: 16.253 distance: 68 - 71: 25.763 distance: 71 - 72: 13.077 distance: 72 - 73: 25.267 distance: 72 - 75: 16.459 distance: 73 - 74: 37.453 distance: 73 - 78: 24.150 distance: 75 - 76: 22.933 distance: 75 - 77: 19.118 distance: 78 - 79: 19.677 distance: 79 - 80: 9.465 distance: 79 - 82: 22.056 distance: 80 - 81: 36.772 distance: 80 - 84: 9.246 distance: 82 - 83: 22.892 distance: 84 - 85: 29.190 distance: 85 - 86: 22.754 distance: 85 - 88: 39.760 distance: 86 - 87: 43.441 distance: 86 - 98: 29.481 distance: 88 - 89: 25.686 distance: 89 - 90: 42.947 distance: 89 - 91: 29.526 distance: 90 - 92: 41.815 distance: 91 - 93: 23.804 distance: 91 - 94: 27.675 distance: 92 - 93: 27.014 distance: 93 - 95: 16.944 distance: 94 - 96: 4.157 distance: 95 - 97: 18.963 distance: 96 - 97: 10.398 distance: 98 - 99: 13.944 distance: 99 - 100: 17.073 distance: 99 - 102: 21.634 distance: 100 - 101: 34.142 distance: 100 - 104: 29.217 distance: 102 - 103: 19.496 distance: 104 - 105: 15.534 distance: 105 - 106: 25.808 distance: 105 - 108: 31.642 distance: 106 - 107: 28.247 distance: 106 - 112: 17.517 distance: 108 - 109: 21.485 distance: 109 - 110: 40.930 distance: 109 - 111: 19.503 distance: 112 - 113: 16.215 distance: 113 - 114: 26.582 distance: 113 - 116: 43.849 distance: 114 - 115: 21.086 distance: 114 - 120: 21.515 distance: 116 - 117: 10.450 distance: 117 - 118: 46.345 distance: 117 - 119: 60.675