Starting phenix.real_space_refine on Thu Sep 18 21:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.map" model { file = "/net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clx_45733/09_2025/9clx_45733.cif" } resolution = 3.65 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= 0.027 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 12818 2.51 5 N 3375 2.21 5 O 3765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20044 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: 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: 5.04, per 1000 atoms: 0.25 Number of scatterers: 20044 At special positions: 0 Unit cell: (97.188, 134.568, 159.132, 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 3765 8.00 N 3375 7.00 C 12818 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=2.04 Simple disulfide: pdb=" SG CYS B 928 " - pdb=" SG CYS B 946 " distance=2.02 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 9 " " NAG A1302 " - " ASN A 82 " " NAG A1303 " - " ASN A 648 " " NAG A1304 " - " ASN A 666 " " NAG B1301 " - " ASN B 9 " " NAG B1302 " - " ASN B 82 " " NAG B1303 " - " 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: 1.87 Conformation dependent library (CDL) restraints added in 688.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 111 helices and 7 sheets defined 65.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 43 removed outlier: 3.578A pdb=" N ASP A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 77 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.588A pdb=" N ASN A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 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 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 261 through 267 removed outlier: 4.235A pdb=" N ASP A 266 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.774A pdb=" N ALA A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.007A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 372 Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.398A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 400 " --> pdb=" O ALA A 396 " (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: 4.348A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 498 through 519 removed outlier: 4.102A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.321A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 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: 3.911A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.582A pdb=" N LYS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.492A pdb=" N ASP A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 removed outlier: 4.091A 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 747 Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.913A pdb=" N GLN A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 792 through 798 removed outlier: 3.847A pdb=" N TRP A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) 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: 3.512A pdb=" N GLY A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.071A pdb=" N ASN A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.547A pdb=" N LEU A 954 " --> pdb=" O ASN A 950 " (cutoff:3.500A) removed outlier: 4.193A 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: 3.515A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.314A 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: 4.015A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 4.215A 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 1066 removed outlier: 3.619A pdb=" N GLU A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP A1061 " --> pdb=" O TYR A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 Processing helix chain 'A' and resid 1096 through 1117 removed outlier: 3.928A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A1112 " --> pdb=" O GLN A1108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.685A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1158 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 removed outlier: 3.507A pdb=" N GLN B 6 " --> pdb=" O PRO B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.715A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 76 through 83 Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 98 through 102 removed outlier: 4.049A pdb=" N ASN B 102 " --> pdb=" O GLY B 99 " (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 200 Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 218 through 238 removed outlier: 3.692A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 4.000A pdb=" N ASP B 266 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 291 through 304 removed outlier: 3.584A pdb=" N ARG B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.983A 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: 3.521A pdb=" N TYR B 369 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 400 removed outlier: 4.024A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 4.623A 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 430 Processing helix chain 'B' and resid 436 through 452 removed outlier: 4.348A pdb=" N TYR B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 5.690A 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: 3.577A pdb=" N ALA B 488 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 489 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 520 removed outlier: 4.269A pdb=" N PHE B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 546 removed outlier: 4.316A 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: 3.743A pdb=" N VAL B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.842A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.520A pdb=" N LYS B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 725 Processing helix chain 'B' and resid 740 through 747 removed outlier: 3.650A pdb=" N THR B 747 " --> pdb=" O ASN B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 771 removed outlier: 4.460A pdb=" N GLN B 771 " --> pdb=" O ARG B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 788 Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 804 through 836 Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 860 through 865 removed outlier: 4.274A pdb=" N ASP B 864 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 882 removed outlier: 3.748A 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: 3.915A pdb=" N ALA B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) removed outlier: 3.614A 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: 3.926A pdb=" N TYR B 970 " --> pdb=" O TYR B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 979 removed outlier: 4.091A pdb=" N GLU B 979 " --> pdb=" O ALA B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 998 removed outlier: 4.802A pdb=" N GLY B 990 " --> pdb=" O HIS B 986 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 993 " --> pdb=" O ILE B 989 " (cutoff:3.500A) removed outlier: 4.236A 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: 3.525A pdb=" N ASP B1019 " --> pdb=" O SER B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1049 removed outlier: 4.127A pdb=" N ASP B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B1042 " --> pdb=" O TYR B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1069 removed outlier: 3.737A pdb=" N TRP B1061 " --> pdb=" O TYR B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1087 Processing helix chain 'B' and resid 1096 through 1118 removed outlier: 3.779A pdb=" N PHE B1100 " --> pdb=" O TYR B1096 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE B1107 " --> pdb=" O PHE B1103 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1143 Processing helix chain 'B' and resid 1144 through 1148 removed outlier: 4.233A pdb=" N ARG B1148 " --> pdb=" O GLY B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1158 removed outlier: 3.735A pdb=" N ALA B1153 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1172 removed outlier: 3.514A pdb=" N LEU B1169 " --> pdb=" O ALA B1165 " (cutoff:3.500A) 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: 5.848A 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: 6.730A 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: 6.284A 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 318 through 319 removed outlier: 7.854A pdb=" N MET B 318 " --> pdb=" O GLN B 347 " (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: 6.534A 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 1056 hydrogen bonds defined for protein. 3093 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: 3.68 Time building geometry restraints manager: 2.50 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: 6377 1.34 - 1.46: 5276 1.46 - 1.59: 8847 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 20644 Sorted by residual: bond pdb=" N TYR B 372 " pdb=" CA TYR B 372 " ideal model delta sigma weight residual 1.464 1.507 -0.044 1.20e-02 6.94e+03 1.32e+01 bond pdb=" C GLN B 367 " pdb=" O GLN B 367 " ideal model delta sigma weight residual 1.236 1.277 -0.040 1.15e-02 7.56e+03 1.24e+01 bond pdb=" N GLN B 367 " pdb=" CA GLN B 367 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.64e+00 bond pdb=" N GLN B 371 " pdb=" CA GLN B 371 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.34e+00 bond pdb=" N TYR B 368 " pdb=" CA TYR B 368 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.97e+00 ... (remaining 20639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 27851 2.89 - 5.78: 238 5.78 - 8.67: 17 8.67 - 11.56: 6 11.56 - 14.45: 1 Bond angle restraints: 28113 Sorted by residual: angle pdb=" N VAL B 268 " pdb=" CA VAL B 268 " pdb=" C VAL B 268 " ideal model delta sigma weight residual 111.88 106.39 5.49 1.06e+00 8.90e-01 2.68e+01 angle pdb=" CB MET A 854 " pdb=" CG MET A 854 " pdb=" SD MET A 854 " ideal model delta sigma weight residual 112.70 127.15 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CB ARG B 942 " pdb=" CG ARG B 942 " pdb=" CD ARG B 942 " ideal model delta sigma weight residual 111.30 121.29 -9.99 2.30e+00 1.89e-01 1.89e+01 angle pdb=" N ILE A1104 " pdb=" CA ILE A1104 " pdb=" C ILE A1104 " ideal model delta sigma weight residual 112.96 108.62 4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" N THR A 878 " pdb=" CA THR A 878 " pdb=" C THR A 878 " ideal model delta sigma weight residual 114.56 109.36 5.20 1.27e+00 6.20e-01 1.68e+01 ... (remaining 28108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10756 17.94 - 35.88: 1395 35.88 - 53.83: 402 53.83 - 71.77: 69 71.77 - 89.71: 21 Dihedral angle restraints: 12643 sinusoidal: 5589 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 -11.04 -74.96 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS B 330 " pdb=" SG CYS B 330 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual -86.00 -148.03 62.03 1 1.00e+01 1.00e-02 5.10e+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 -146.97 60.97 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 12640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2515 0.055 - 0.110: 453 0.110 - 0.165: 53 0.165 - 0.219: 4 0.219 - 0.274: 5 Chirality restraints: 3030 Sorted by residual: chirality pdb=" CB VAL B 268 " pdb=" CA VAL B 268 " pdb=" CG1 VAL B 268 " pdb=" CG2 VAL B 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 289 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 NAG Q 2 " pdb=" C1 NAG Q 2 " pdb=" C3 NAG Q 2 " pdb=" N2 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3027 not shown) Planarity restraints: 3622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 372 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C TYR B 372 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR B 372 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 373 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 907 " 0.035 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A 908 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 820 " 0.020 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR B 820 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 820 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 820 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 820 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 820 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 820 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 820 " 0.002 2.00e-02 2.50e+03 ... (remaining 3619 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3034 2.75 - 3.29: 20381 3.29 - 3.83: 35410 3.83 - 4.36: 38397 4.36 - 4.90: 66518 Nonbonded interactions: 163740 Sorted by model distance: nonbonded pdb=" OG1 THR A 352 " pdb=" OD1 ASP A 354 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU A 161 " pdb=" OH TYR A 607 " model vdw 2.219 3.040 nonbonded pdb=" O PHE A 574 " pdb=" OG1 THR A 578 " model vdw 2.242 3.040 nonbonded pdb=" O TYR B 627 " pdb=" OG SER B 631 " model vdw 2.261 3.040 nonbonded pdb=" O PHE B 574 " pdb=" OG1 THR B 578 " model vdw 2.265 3.040 ... (remaining 163735 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 1304)) 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 1303)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.110 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.004 0.044 20691 Z= 0.174 Angle : 0.686 14.450 28243 Z= 0.343 Chirality : 0.043 0.274 3030 Planarity : 0.004 0.054 3603 Dihedral : 17.075 89.710 8066 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.75 % Allowed : 22.86 % Favored : 73.39 % 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: 0.01 (0.18), residues: 2396 helix: 1.03 (0.14), residues: 1474 sheet: None (None), residues: 0 loop : -1.73 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 942 TYR 0.035 0.002 TYR B 820 PHE 0.020 0.002 PHE B 178 TRP 0.023 0.001 TRP A 80 HIS 0.007 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00381 (20644) covalent geometry : angle 0.66948 (28113) SS BOND : bond 0.00458 ( 11) SS BOND : angle 1.74636 ( 22) hydrogen bonds : bond 0.12928 ( 1056) hydrogen bonds : angle 5.66770 ( 3093) link_BETA1-4 : bond 0.00631 ( 16) link_BETA1-4 : angle 2.80872 ( 48) link_BETA1-6 : bond 0.00175 ( 1) link_BETA1-6 : angle 1.25051 ( 3) link_NAG-ASN : bond 0.00236 ( 19) link_NAG-ASN : angle 2.08717 ( 57) *********************** 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 291 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 0.549 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: A 83 PHE cc_start: 0.7757 (m-80) cc_final: 0.7426 (m-80) REVERT: A 242 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7393 (mt) REVERT: A 256 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7091 (ttt) REVERT: A 644 ASN cc_start: 0.7380 (m-40) cc_final: 0.6821 (m-40) REVERT: A 659 GLN cc_start: 0.6531 (pp30) cc_final: 0.6208 (tp40) REVERT: A 682 GLN cc_start: 0.7878 (mt0) cc_final: 0.6623 (tp40) REVERT: A 720 THR cc_start: 0.7989 (m) cc_final: 0.7667 (p) REVERT: A 878 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 881 MET cc_start: 0.8124 (pmm) cc_final: 0.6661 (ptt) REVERT: A 893 LYS cc_start: 0.8553 (tptm) cc_final: 0.8096 (tptp) REVERT: A 1140 THR cc_start: 0.8665 (t) cc_final: 0.8293 (m) REVERT: B 188 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6572 (mp10) REVERT: B 228 PHE cc_start: 0.7573 (t80) cc_final: 0.7286 (t80) REVERT: B 253 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7455 (pp) REVERT: B 283 MET cc_start: 0.5637 (mmp) cc_final: 0.3227 (mtp) REVERT: B 294 PHE cc_start: 0.7804 (m-80) cc_final: 0.7587 (m-80) REVERT: B 541 ARG cc_start: 0.6973 (ttt180) cc_final: 0.5672 (mtt180) REVERT: B 652 GLU cc_start: 0.6392 (pp20) cc_final: 0.6087 (pp20) REVERT: B 854 MET cc_start: 0.8044 (tpt) cc_final: 0.7827 (tpt) REVERT: B 875 MET cc_start: 0.7117 (tmm) cc_final: 0.6418 (tpp) REVERT: B 890 ARG cc_start: 0.8218 (ptt90) cc_final: 0.7555 (ttt-90) REVERT: B 961 MET cc_start: 0.8843 (tpp) cc_final: 0.8447 (ttm) REVERT: B 991 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7021 (t0) REVERT: B 1020 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5630 (mt) REVERT: B 1122 PRO cc_start: 0.7978 (Cg_exo) cc_final: 0.7721 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8309 (ptm) cc_final: 0.7901 (ptm) REVERT: B 1146 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: B 1184 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6367 (mp0) outliers start: 78 outliers final: 64 residues processed: 272 average time/residue: 0.1428 time to fit residues: 61.3552 Evaluate side-chains 277 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 205 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 877 THR Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1020 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 339 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 659 GLN A 684 GLN A1018 HIS A1021 ASN B 292 HIS B 331 HIS B 365 HIS ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS B 642 ASN ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116892 restraints weight = 29640.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116227 restraints weight = 28107.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116997 restraints weight = 32098.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119000 restraints weight = 19889.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119471 restraints weight = 16130.105| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20691 Z= 0.143 Angle : 0.640 9.678 28243 Z= 0.313 Chirality : 0.042 0.231 3030 Planarity : 0.004 0.052 3603 Dihedral : 8.470 80.782 3500 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.76 % Allowed : 22.38 % Favored : 72.86 % 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: 0.13 (0.18), residues: 2396 helix: 1.17 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -1.81 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 942 TYR 0.026 0.001 TYR B 820 PHE 0.017 0.001 PHE B 178 TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00325 (20644) covalent geometry : angle 0.62139 (28113) SS BOND : bond 0.00403 ( 11) SS BOND : angle 1.49585 ( 22) hydrogen bonds : bond 0.04346 ( 1056) hydrogen bonds : angle 4.42746 ( 3093) link_BETA1-4 : bond 0.00626 ( 16) link_BETA1-4 : angle 2.85494 ( 48) link_BETA1-6 : bond 0.00286 ( 1) link_BETA1-6 : angle 1.21457 ( 3) link_NAG-ASN : bond 0.00246 ( 19) link_NAG-ASN : angle 2.13768 ( 57) *********************** 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 309 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 0.780 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: A 83 PHE cc_start: 0.7676 (m-80) cc_final: 0.7395 (m-80) REVERT: A 539 LYS cc_start: 0.6294 (pttt) cc_final: 0.6083 (pttt) REVERT: A 542 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7547 (mmtm) REVERT: A 644 ASN cc_start: 0.7380 (m-40) cc_final: 0.6772 (m110) REVERT: A 682 GLN cc_start: 0.7770 (mt0) cc_final: 0.6646 (tp40) REVERT: A 854 MET cc_start: 0.6758 (tpp) cc_final: 0.6532 (tpp) REVERT: A 881 MET cc_start: 0.8195 (pmm) cc_final: 0.6864 (ptt) REVERT: A 893 LYS cc_start: 0.8532 (tptm) cc_final: 0.8078 (tptp) REVERT: A 1140 THR cc_start: 0.8654 (t) cc_final: 0.8390 (m) REVERT: A 1154 MET cc_start: 0.7744 (tpt) cc_final: 0.7146 (tpt) REVERT: A 1156 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 228 PHE cc_start: 0.7473 (t80) cc_final: 0.7200 (t80) REVERT: B 253 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7470 (pp) REVERT: B 283 MET cc_start: 0.5867 (mmp) cc_final: 0.3495 (mtp) REVERT: B 462 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8531 (t0) REVERT: B 527 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5952 (pm20) REVERT: B 541 ARG cc_start: 0.6952 (ttt180) cc_final: 0.5813 (mtt180) REVERT: B 658 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6325 (mp) REVERT: B 875 MET cc_start: 0.7079 (tmm) cc_final: 0.6461 (tpp) REVERT: B 890 ARG cc_start: 0.8238 (ptt90) cc_final: 0.7996 (ttt-90) REVERT: B 1122 PRO cc_start: 0.7967 (Cg_exo) cc_final: 0.7713 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8301 (ptm) cc_final: 0.7891 (ptm) REVERT: B 1146 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6051 (m-80) REVERT: B 1184 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6460 (mp0) outliers start: 99 outliers final: 58 residues processed: 295 average time/residue: 0.1338 time to fit residues: 62.4644 Evaluate side-chains 260 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 683 LEU 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 904 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 26 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 117 optimal weight: 0.0670 chunk 215 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 ASN B1196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116589 restraints weight = 30535.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114542 restraints weight = 34874.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116026 restraints weight = 36387.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117400 restraints weight = 21995.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118262 restraints weight = 18873.934| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20691 Z= 0.173 Angle : 0.645 9.796 28243 Z= 0.314 Chirality : 0.043 0.234 3030 Planarity : 0.004 0.053 3603 Dihedral : 7.620 59.424 3440 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.63 % Allowed : 22.47 % Favored : 71.90 % 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: 0.12 (0.18), residues: 2396 helix: 1.17 (0.14), residues: 1487 sheet: None (None), residues: 0 loop : -1.81 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 942 TYR 0.026 0.002 TYR B 970 PHE 0.022 0.002 PHE B 178 TRP 0.018 0.001 TRP B 643 HIS 0.006 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00410 (20644) covalent geometry : angle 0.62674 (28113) SS BOND : bond 0.00414 ( 11) SS BOND : angle 1.48551 ( 22) hydrogen bonds : bond 0.04294 ( 1056) hydrogen bonds : angle 4.35986 ( 3093) link_BETA1-4 : bond 0.00627 ( 16) link_BETA1-4 : angle 2.82445 ( 48) link_BETA1-6 : bond 0.00208 ( 1) link_BETA1-6 : angle 1.26390 ( 3) link_NAG-ASN : bond 0.00286 ( 19) link_NAG-ASN : angle 2.18765 ( 57) *********************** 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 321 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 204 time to evaluate : 0.768 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: A 63 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: A 83 PHE cc_start: 0.7751 (m-80) cc_final: 0.7390 (m-80) REVERT: A 508 GLN cc_start: 0.7549 (pt0) cc_final: 0.7271 (pt0) REVERT: A 539 LYS cc_start: 0.6460 (pttt) cc_final: 0.6241 (pttt) REVERT: A 542 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7500 (mmtm) REVERT: A 644 ASN cc_start: 0.7495 (m-40) cc_final: 0.6930 (m110) REVERT: A 659 GLN cc_start: 0.7138 (pp30) cc_final: 0.6565 (tp-100) REVERT: A 682 GLN cc_start: 0.7834 (mt0) cc_final: 0.6687 (tp40) REVERT: A 816 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 854 MET cc_start: 0.7053 (tpp) cc_final: 0.6613 (tpp) REVERT: A 881 MET cc_start: 0.8236 (pmm) cc_final: 0.7023 (ptt) REVERT: A 893 LYS cc_start: 0.8547 (tptm) cc_final: 0.8094 (tptp) REVERT: A 936 TYR cc_start: 0.6862 (m-80) cc_final: 0.6616 (m-80) REVERT: A 1140 THR cc_start: 0.8602 (t) cc_final: 0.8369 (m) REVERT: A 1154 MET cc_start: 0.7607 (tpt) cc_final: 0.6810 (tpt) REVERT: A 1156 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 97 THR cc_start: 0.8767 (m) cc_final: 0.8544 (t) REVERT: B 253 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7665 (pp) REVERT: B 283 MET cc_start: 0.5867 (mmp) cc_final: 0.3414 (mtp) REVERT: B 344 ARG cc_start: 0.6795 (ttt-90) cc_final: 0.6533 (ttt-90) REVERT: B 462 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 662 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4723 (tmm) REVERT: B 875 MET cc_start: 0.7171 (tmm) cc_final: 0.6542 (tpp) REVERT: B 939 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7452 (tttt) REVERT: B 968 MET cc_start: 0.7150 (ttm) cc_final: 0.6709 (mtt) REVERT: B 1122 PRO cc_start: 0.7995 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: B 1129 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6379 (t80) REVERT: B 1142 MET cc_start: 0.8313 (ptm) cc_final: 0.7909 (ptm) REVERT: B 1146 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6059 (m-80) outliers start: 117 outliers final: 80 residues processed: 299 average time/residue: 0.1399 time to fit residues: 66.9925 Evaluate side-chains 277 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 189 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 370 LEU 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 401 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 387 PHE 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 414 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL 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 904 LEU Chi-restraints excluded: chain B residue 941 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 1 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 78 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 659 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117187 restraints weight = 29857.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115705 restraints weight = 30754.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117398 restraints weight = 30395.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118068 restraints weight = 19853.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120091 restraints weight = 17665.556| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20691 Z= 0.132 Angle : 0.619 9.868 28243 Z= 0.299 Chirality : 0.041 0.229 3030 Planarity : 0.004 0.056 3603 Dihedral : 7.513 59.638 3438 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.62 % Allowed : 24.01 % Favored : 71.37 % 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: 0.23 (0.18), residues: 2396 helix: 1.24 (0.14), residues: 1490 sheet: None (None), residues: 0 loop : -1.76 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 942 TYR 0.022 0.001 TYR A1195 PHE 0.021 0.001 PHE B 178 TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00299 (20644) covalent geometry : angle 0.60003 (28113) SS BOND : bond 0.00353 ( 11) SS BOND : angle 1.62601 ( 22) hydrogen bonds : bond 0.03949 ( 1056) hydrogen bonds : angle 4.23788 ( 3093) link_BETA1-4 : bond 0.00624 ( 16) link_BETA1-4 : angle 2.80528 ( 48) link_BETA1-6 : bond 0.00272 ( 1) link_BETA1-6 : angle 1.23011 ( 3) link_NAG-ASN : bond 0.00252 ( 19) link_NAG-ASN : angle 2.13798 ( 57) *********************** 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 305 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 209 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: A 83 PHE cc_start: 0.7664 (m-80) cc_final: 0.7347 (m-80) REVERT: A 542 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7337 (mmtm) REVERT: A 644 ASN cc_start: 0.7428 (m-40) cc_final: 0.6835 (m110) REVERT: A 682 GLN cc_start: 0.7789 (mt0) cc_final: 0.6711 (tp40) REVERT: A 854 MET cc_start: 0.7001 (tpp) cc_final: 0.6422 (tpp) REVERT: A 881 MET cc_start: 0.8208 (pmm) cc_final: 0.7246 (ptt) REVERT: A 893 LYS cc_start: 0.8540 (tptm) cc_final: 0.8082 (tptp) REVERT: A 936 TYR cc_start: 0.6755 (m-80) cc_final: 0.6467 (m-80) REVERT: A 941 PHE cc_start: 0.6851 (m-80) cc_final: 0.6431 (m-80) REVERT: A 1140 THR cc_start: 0.8547 (t) cc_final: 0.8294 (m) REVERT: A 1156 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 228 PHE cc_start: 0.7341 (t80) cc_final: 0.7129 (t80) REVERT: B 253 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7612 (pp) REVERT: B 283 MET cc_start: 0.5913 (mmp) cc_final: 0.3476 (mtp) REVERT: B 344 ARG cc_start: 0.6751 (ttt-90) cc_final: 0.6461 (ttt-90) REVERT: B 462 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8466 (t0) REVERT: B 541 ARG cc_start: 0.6958 (ttt180) cc_final: 0.5879 (mtt180) REVERT: B 662 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4676 (tmm) REVERT: B 854 MET cc_start: 0.7987 (tpt) cc_final: 0.7757 (tpt) REVERT: B 875 MET cc_start: 0.7197 (tmm) cc_final: 0.6602 (tpp) REVERT: B 935 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7616 (p90) REVERT: B 961 MET cc_start: 0.8847 (tpp) cc_final: 0.8256 (ttm) REVERT: B 1122 PRO cc_start: 0.8024 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8334 (ptm) cc_final: 0.7933 (ptm) REVERT: B 1146 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: B 1184 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6394 (mp0) outliers start: 96 outliers final: 71 residues processed: 284 average time/residue: 0.1383 time to fit residues: 63.1176 Evaluate side-chains 272 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 194 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL 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 877 THR Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 941 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 38 optimal weight: 0.0030 chunk 152 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117694 restraints weight = 29764.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116844 restraints weight = 29802.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118060 restraints weight = 31321.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119285 restraints weight = 19122.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120308 restraints weight = 16692.282| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20691 Z= 0.129 Angle : 0.616 11.981 28243 Z= 0.297 Chirality : 0.041 0.234 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.364 59.788 3432 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.49 % Allowed : 23.82 % Favored : 70.69 % 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: 0.27 (0.18), residues: 2396 helix: 1.27 (0.14), residues: 1499 sheet: None (None), residues: 0 loop : -1.75 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 942 TYR 0.023 0.001 TYR A1195 PHE 0.021 0.001 PHE B 178 TRP 0.045 0.001 TRP A 643 HIS 0.006 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00292 (20644) covalent geometry : angle 0.59734 (28113) SS BOND : bond 0.00381 ( 11) SS BOND : angle 1.52117 ( 22) hydrogen bonds : bond 0.03844 ( 1056) hydrogen bonds : angle 4.19526 ( 3093) link_BETA1-4 : bond 0.00630 ( 16) link_BETA1-4 : angle 2.78068 ( 48) link_BETA1-6 : bond 0.00277 ( 1) link_BETA1-6 : angle 1.24707 ( 3) link_NAG-ASN : bond 0.00248 ( 19) link_NAG-ASN : angle 2.10961 ( 57) *********************** 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 329 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 215 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7293 (mpt180) cc_final: 0.6865 (ptp-170) REVERT: A 63 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: A 293 MET cc_start: 0.6136 (ptp) cc_final: 0.5637 (ptt) REVERT: A 380 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7458 (mmm-85) REVERT: A 542 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7349 (mmtm) REVERT: A 644 ASN cc_start: 0.7326 (m-40) cc_final: 0.6766 (m-40) REVERT: A 659 GLN cc_start: 0.7097 (pp30) cc_final: 0.6585 (tp-100) REVERT: A 682 GLN cc_start: 0.7779 (mt0) cc_final: 0.6698 (tp40) REVERT: A 854 MET cc_start: 0.7046 (tpp) cc_final: 0.6400 (tpp) REVERT: A 881 MET cc_start: 0.8188 (pmm) cc_final: 0.7247 (ptt) REVERT: A 883 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7699 (pptt) REVERT: A 886 TRP cc_start: 0.7319 (m100) cc_final: 0.7113 (m100) REVERT: A 893 LYS cc_start: 0.8526 (tptm) cc_final: 0.8082 (tptp) REVERT: A 941 PHE cc_start: 0.6677 (m-80) cc_final: 0.6396 (m-80) REVERT: A 1140 THR cc_start: 0.8635 (t) cc_final: 0.8427 (m) REVERT: A 1154 MET cc_start: 0.7523 (tpt) cc_final: 0.7300 (tpt) REVERT: A 1156 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 228 PHE cc_start: 0.7382 (t80) cc_final: 0.7104 (t80) REVERT: B 253 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7608 (pp) REVERT: B 283 MET cc_start: 0.5939 (mmp) cc_final: 0.3456 (mtp) REVERT: B 344 ARG cc_start: 0.6684 (ttt-90) cc_final: 0.6407 (ttt-90) REVERT: B 415 THR cc_start: 0.6345 (OUTLIER) cc_final: 0.5355 (p) REVERT: B 462 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8482 (t0) REVERT: B 541 ARG cc_start: 0.6844 (ttt180) cc_final: 0.5875 (mtt180) REVERT: B 662 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4721 (tmm) REVERT: B 875 MET cc_start: 0.7283 (tmm) cc_final: 0.6668 (tpp) REVERT: B 935 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7646 (p90) REVERT: B 939 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7412 (tttt) REVERT: B 991 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7009 (t0) REVERT: B 1122 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7698 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8260 (ptm) cc_final: 0.7888 (ptm) REVERT: B 1146 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: B 1184 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6404 (mp0) outliers start: 114 outliers final: 80 residues processed: 306 average time/residue: 0.1312 time to fit residues: 63.8037 Evaluate side-chains 285 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 195 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL 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 877 THR Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116076 restraints weight = 29817.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114160 restraints weight = 32338.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116040 restraints weight = 31215.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116502 restraints weight = 20821.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118758 restraints weight = 18260.730| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20691 Z= 0.162 Angle : 0.639 9.767 28243 Z= 0.311 Chirality : 0.043 0.240 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.348 58.145 3430 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.44 % Allowed : 23.58 % Favored : 70.98 % 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: 0.19 (0.18), residues: 2396 helix: 1.21 (0.14), residues: 1499 sheet: None (None), residues: 0 loop : -1.80 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 942 TYR 0.022 0.002 TYR A1195 PHE 0.020 0.002 PHE A 10 TRP 0.033 0.001 TRP A 643 HIS 0.006 0.001 HIS B 849 Details of bonding type rmsd covalent geometry : bond 0.00384 (20644) covalent geometry : angle 0.62133 (28113) SS BOND : bond 0.00412 ( 11) SS BOND : angle 1.58384 ( 22) hydrogen bonds : bond 0.03989 ( 1056) hydrogen bonds : angle 4.21078 ( 3093) link_BETA1-4 : bond 0.00624 ( 16) link_BETA1-4 : angle 2.77532 ( 48) link_BETA1-6 : bond 0.00218 ( 1) link_BETA1-6 : angle 1.27253 ( 3) link_NAG-ASN : bond 0.00275 ( 19) link_NAG-ASN : angle 2.13602 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 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: 113 poor density : 206 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7257 (mpt180) cc_final: 0.6797 (ptp-170) REVERT: A 63 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 293 MET cc_start: 0.6240 (ptp) cc_final: 0.5618 (ptt) REVERT: A 508 GLN cc_start: 0.7487 (pt0) cc_final: 0.7174 (pt0) REVERT: A 542 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7350 (mmtm) REVERT: A 644 ASN cc_start: 0.7460 (m-40) cc_final: 0.6884 (m-40) REVERT: A 682 GLN cc_start: 0.7784 (mt0) cc_final: 0.7165 (tp40) REVERT: A 854 MET cc_start: 0.7166 (tpp) cc_final: 0.6444 (tpp) REVERT: A 881 MET cc_start: 0.8164 (pmm) cc_final: 0.7294 (ptt) REVERT: A 883 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7704 (pptt) REVERT: A 886 TRP cc_start: 0.7269 (m100) cc_final: 0.7061 (m100) REVERT: A 893 LYS cc_start: 0.8537 (tptm) cc_final: 0.8098 (tptp) REVERT: A 1140 THR cc_start: 0.8745 (t) cc_final: 0.8484 (m) REVERT: A 1156 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 228 PHE cc_start: 0.7530 (t80) cc_final: 0.7272 (t80) REVERT: B 253 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7721 (pp) REVERT: B 283 MET cc_start: 0.5974 (mmp) cc_final: 0.3429 (mtp) REVERT: B 344 ARG cc_start: 0.6678 (ttt-90) cc_final: 0.6309 (ttt-90) REVERT: B 415 THR cc_start: 0.6372 (OUTLIER) cc_final: 0.5406 (p) REVERT: B 462 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 662 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4738 (tmm) REVERT: B 875 MET cc_start: 0.7322 (tmm) cc_final: 0.6703 (tpp) REVERT: B 933 TRP cc_start: 0.8349 (m100) cc_final: 0.8126 (m100) REVERT: B 935 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7652 (p90) REVERT: B 939 LYS cc_start: 0.7760 (ttpt) cc_final: 0.7376 (tttt) REVERT: B 1122 PRO cc_start: 0.7978 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8298 (ptm) cc_final: 0.7984 (ptm) REVERT: B 1146 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: B 1184 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6503 (mp0) outliers start: 113 outliers final: 84 residues processed: 298 average time/residue: 0.1308 time to fit residues: 62.4895 Evaluate side-chains 288 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 195 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 370 LEU 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 405 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 727 VAL 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 877 THR Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 176 optimal weight: 0.0010 chunk 225 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN B1162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.158614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117624 restraints weight = 29748.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116521 restraints weight = 30386.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117903 restraints weight = 31596.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119068 restraints weight = 19374.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120185 restraints weight = 16919.746| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20691 Z= 0.131 Angle : 0.628 9.737 28243 Z= 0.304 Chirality : 0.042 0.226 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.275 57.785 3430 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.86 % Allowed : 24.11 % Favored : 71.03 % 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: 0.27 (0.18), residues: 2396 helix: 1.28 (0.14), residues: 1499 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 942 TYR 0.024 0.001 TYR A1195 PHE 0.019 0.001 PHE A 10 TRP 0.024 0.001 TRP A 643 HIS 0.008 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00297 (20644) covalent geometry : angle 0.61070 (28113) SS BOND : bond 0.00383 ( 11) SS BOND : angle 1.48243 ( 22) hydrogen bonds : bond 0.03814 ( 1056) hydrogen bonds : angle 4.15881 ( 3093) link_BETA1-4 : bond 0.00642 ( 16) link_BETA1-4 : angle 2.75144 ( 48) link_BETA1-6 : bond 0.00264 ( 1) link_BETA1-6 : angle 1.23703 ( 3) link_NAG-ASN : bond 0.00245 ( 19) link_NAG-ASN : angle 2.09983 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 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 303 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 202 time to evaluate : 0.516 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: A 52 ARG cc_start: 0.7249 (mpt180) cc_final: 0.6791 (ptp-170) REVERT: A 63 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: A 81 GLN cc_start: 0.8054 (tp40) cc_final: 0.7749 (tm-30) REVERT: A 293 MET cc_start: 0.6359 (ptp) cc_final: 0.5748 (ptt) REVERT: A 542 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7330 (mmtm) REVERT: A 644 ASN cc_start: 0.7463 (m-40) cc_final: 0.6874 (m-40) REVERT: A 854 MET cc_start: 0.7111 (tpp) cc_final: 0.6850 (tpt) REVERT: A 881 MET cc_start: 0.8087 (pmm) cc_final: 0.7283 (ptt) REVERT: A 883 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7705 (pptt) REVERT: A 886 TRP cc_start: 0.7264 (m100) cc_final: 0.7017 (m100) REVERT: A 893 LYS cc_start: 0.8525 (tptm) cc_final: 0.8077 (tptp) REVERT: A 1140 THR cc_start: 0.8749 (t) cc_final: 0.8467 (m) REVERT: A 1156 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 228 PHE cc_start: 0.7355 (t80) cc_final: 0.7063 (t80) REVERT: B 253 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7680 (pp) REVERT: B 283 MET cc_start: 0.5963 (mmp) cc_final: 0.3417 (mtp) REVERT: B 344 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.6270 (ttt-90) REVERT: B 415 THR cc_start: 0.6301 (OUTLIER) cc_final: 0.5301 (p) REVERT: B 462 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 875 MET cc_start: 0.7321 (tmm) cc_final: 0.6723 (tpp) REVERT: B 935 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7685 (p90) REVERT: B 961 MET cc_start: 0.8815 (tpp) cc_final: 0.8606 (ttm) REVERT: B 968 MET cc_start: 0.6510 (ttm) cc_final: 0.6000 (mtt) REVERT: B 991 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7043 (t0) REVERT: B 1122 PRO cc_start: 0.7959 (Cg_exo) cc_final: 0.7672 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8204 (ptm) cc_final: 0.7887 (ptm) REVERT: B 1146 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.5951 (m-80) outliers start: 101 outliers final: 78 residues processed: 284 average time/residue: 0.1365 time to fit residues: 62.2775 Evaluate side-chains 284 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 197 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 345 ILE 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 421 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL 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 877 THR Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 181 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118302 restraints weight = 29657.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117438 restraints weight = 30334.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118766 restraints weight = 30975.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119749 restraints weight = 19203.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121534 restraints weight = 16962.546| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20691 Z= 0.128 Angle : 0.635 12.013 28243 Z= 0.305 Chirality : 0.041 0.232 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.159 57.748 3427 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.72 % Allowed : 24.64 % Favored : 70.64 % 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: 0.28 (0.18), residues: 2396 helix: 1.28 (0.14), residues: 1506 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 942 TYR 0.024 0.001 TYR A1195 PHE 0.020 0.001 PHE A 10 TRP 0.023 0.001 TRP B 643 HIS 0.008 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00289 (20644) covalent geometry : angle 0.61718 (28113) SS BOND : bond 0.00347 ( 11) SS BOND : angle 1.55274 ( 22) hydrogen bonds : bond 0.03722 ( 1056) hydrogen bonds : angle 4.12904 ( 3093) link_BETA1-4 : bond 0.00622 ( 16) link_BETA1-4 : angle 2.73220 ( 48) link_BETA1-6 : bond 0.00269 ( 1) link_BETA1-6 : angle 1.23955 ( 3) link_NAG-ASN : bond 0.00243 ( 19) link_NAG-ASN : angle 2.07914 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 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 303 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.748 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: A 54 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7608 (mm-40) REVERT: A 63 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: A 81 GLN cc_start: 0.8006 (tp40) cc_final: 0.7726 (tm-30) REVERT: A 293 MET cc_start: 0.6354 (ptp) cc_final: 0.5760 (ptt) REVERT: A 343 PHE cc_start: 0.6636 (m-80) cc_final: 0.6186 (m-80) REVERT: A 542 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7341 (mmtm) REVERT: A 644 ASN cc_start: 0.7423 (m-40) cc_final: 0.6837 (m-40) REVERT: A 659 GLN cc_start: 0.6813 (pp30) cc_final: 0.6360 (tp40) REVERT: A 854 MET cc_start: 0.7110 (tpp) cc_final: 0.6432 (tpp) REVERT: A 881 MET cc_start: 0.8086 (pmm) cc_final: 0.7311 (ptt) REVERT: A 883 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7649 (pptt) REVERT: A 886 TRP cc_start: 0.7244 (m100) cc_final: 0.7017 (m100) REVERT: A 893 LYS cc_start: 0.8510 (tptm) cc_final: 0.8062 (tptp) REVERT: A 1140 THR cc_start: 0.8719 (t) cc_final: 0.8416 (m) REVERT: A 1156 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (mp) REVERT: B 225 LEU cc_start: 0.7327 (tt) cc_final: 0.6838 (tp) REVERT: B 228 PHE cc_start: 0.7284 (t80) cc_final: 0.6988 (t80) REVERT: B 253 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7643 (pp) REVERT: B 283 MET cc_start: 0.5904 (mmp) cc_final: 0.3458 (mtp) REVERT: B 344 ARG cc_start: 0.6624 (ttt-90) cc_final: 0.6284 (ttt-90) REVERT: B 415 THR cc_start: 0.6318 (OUTLIER) cc_final: 0.5331 (p) REVERT: B 462 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 875 MET cc_start: 0.7349 (tmm) cc_final: 0.6777 (tpp) REVERT: B 935 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7696 (p90) REVERT: B 963 HIS cc_start: 0.5808 (m170) cc_final: 0.5430 (m170) REVERT: B 968 MET cc_start: 0.6652 (ttm) cc_final: 0.6261 (mtt) REVERT: B 991 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7034 (t0) REVERT: B 1122 PRO cc_start: 0.7978 (Cg_exo) cc_final: 0.7727 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8180 (ptm) cc_final: 0.7876 (ptm) REVERT: B 1146 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: B 1184 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6428 (mp0) outliers start: 98 outliers final: 79 residues processed: 285 average time/residue: 0.1352 time to fit residues: 62.0477 Evaluate side-chains 284 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 355 GLN 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 422 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 877 THR Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 193 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 146 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 221 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118293 restraints weight = 29694.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117466 restraints weight = 30325.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118776 restraints weight = 31281.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119964 restraints weight = 18970.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121517 restraints weight = 16644.367| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20691 Z= 0.130 Angle : 0.644 10.406 28243 Z= 0.306 Chirality : 0.042 0.231 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.051 58.143 3424 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.76 % Allowed : 24.93 % Favored : 70.31 % 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: 0.30 (0.18), residues: 2396 helix: 1.29 (0.14), residues: 1507 sheet: None (None), residues: 0 loop : -1.78 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 942 TYR 0.024 0.001 TYR A1195 PHE 0.024 0.001 PHE B 301 TRP 0.024 0.001 TRP B 643 HIS 0.007 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00297 (20644) covalent geometry : angle 0.62697 (28113) SS BOND : bond 0.00372 ( 11) SS BOND : angle 1.51789 ( 22) hydrogen bonds : bond 0.03704 ( 1056) hydrogen bonds : angle 4.11578 ( 3093) link_BETA1-4 : bond 0.00630 ( 16) link_BETA1-4 : angle 2.70675 ( 48) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.24536 ( 3) link_NAG-ASN : bond 0.00241 ( 19) link_NAG-ASN : angle 2.05618 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 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: 99 poor density : 203 time to evaluate : 0.623 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: A 63 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 293 MET cc_start: 0.6380 (ptp) cc_final: 0.5793 (ptt) REVERT: A 542 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7343 (mmtm) REVERT: A 644 ASN cc_start: 0.7375 (m-40) cc_final: 0.6796 (m-40) REVERT: A 854 MET cc_start: 0.7080 (tpp) cc_final: 0.6805 (tpt) REVERT: A 881 MET cc_start: 0.8064 (pmm) cc_final: 0.7321 (ptt) REVERT: A 883 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7652 (pptt) REVERT: A 886 TRP cc_start: 0.7238 (m100) cc_final: 0.7017 (m100) REVERT: A 893 LYS cc_start: 0.8513 (tptm) cc_final: 0.8059 (tptp) REVERT: A 1140 THR cc_start: 0.8762 (t) cc_final: 0.8431 (m) REVERT: B 89 ARG cc_start: 0.6947 (mmt180) cc_final: 0.6541 (mmm-85) REVERT: B 225 LEU cc_start: 0.7375 (tt) cc_final: 0.6881 (tp) REVERT: B 228 PHE cc_start: 0.7270 (t80) cc_final: 0.7005 (t80) REVERT: B 253 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7639 (pp) REVERT: B 283 MET cc_start: 0.5940 (mmp) cc_final: 0.3464 (mtp) REVERT: B 344 ARG cc_start: 0.6582 (ttt-90) cc_final: 0.6254 (ttt-90) REVERT: B 415 THR cc_start: 0.6328 (OUTLIER) cc_final: 0.5324 (p) REVERT: B 462 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 737 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7983 (tp) REVERT: B 875 MET cc_start: 0.7352 (tmm) cc_final: 0.6794 (tpp) REVERT: B 935 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7676 (p90) REVERT: B 968 MET cc_start: 0.6717 (ttm) cc_final: 0.6326 (mtt) REVERT: B 991 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7043 (t0) REVERT: B 1122 PRO cc_start: 0.7971 (Cg_exo) cc_final: 0.7708 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8148 (ptm) cc_final: 0.7853 (ptm) REVERT: B 1146 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: B 1168 MET cc_start: 0.8649 (tpp) cc_final: 0.7629 (ttt) REVERT: B 1184 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6448 (mp0) outliers start: 99 outliers final: 84 residues processed: 285 average time/residue: 0.1324 time to fit residues: 60.7406 Evaluate side-chains 287 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 194 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 877 THR Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 113 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN ** B1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117855 restraints weight = 29883.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116396 restraints weight = 30847.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118114 restraints weight = 31169.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118685 restraints weight = 19522.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121160 restraints weight = 17535.440| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20691 Z= 0.141 Angle : 0.652 12.709 28243 Z= 0.312 Chirality : 0.042 0.232 3030 Planarity : 0.004 0.059 3603 Dihedral : 7.037 58.923 3423 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.86 % Allowed : 24.98 % Favored : 70.16 % 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: 0.27 (0.18), residues: 2396 helix: 1.26 (0.14), residues: 1505 sheet: -3.36 (1.58), residues: 10 loop : -1.74 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 942 TYR 0.022 0.002 TYR A1195 PHE 0.021 0.002 PHE B 178 TRP 0.026 0.001 TRP B 643 HIS 0.007 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00329 (20644) covalent geometry : angle 0.63615 (28113) SS BOND : bond 0.00369 ( 11) SS BOND : angle 1.50820 ( 22) hydrogen bonds : bond 0.03783 ( 1056) hydrogen bonds : angle 4.13088 ( 3093) link_BETA1-4 : bond 0.00629 ( 16) link_BETA1-4 : angle 2.69868 ( 48) link_BETA1-6 : bond 0.00247 ( 1) link_BETA1-6 : angle 1.25746 ( 3) link_NAG-ASN : bond 0.00244 ( 19) link_NAG-ASN : angle 2.05727 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 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 301 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 200 time to evaluate : 0.781 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: A 52 ARG cc_start: 0.7202 (mpt180) cc_final: 0.6764 (ptp-170) REVERT: A 63 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 542 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7312 (mmtm) REVERT: A 644 ASN cc_start: 0.7361 (m-40) cc_final: 0.6774 (m-40) REVERT: A 659 GLN cc_start: 0.7281 (pp30) cc_final: 0.6781 (pm20) REVERT: A 854 MET cc_start: 0.7091 (tpp) cc_final: 0.6828 (tpt) REVERT: A 881 MET cc_start: 0.8118 (pmm) cc_final: 0.7327 (ptt) REVERT: A 883 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7664 (pptt) REVERT: A 886 TRP cc_start: 0.7281 (m100) cc_final: 0.7033 (m100) REVERT: A 893 LYS cc_start: 0.8516 (tptm) cc_final: 0.8062 (tptp) REVERT: A 1140 THR cc_start: 0.8713 (t) cc_final: 0.8373 (m) REVERT: B 225 LEU cc_start: 0.7388 (tt) cc_final: 0.6890 (tp) REVERT: B 253 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7710 (pp) REVERT: B 283 MET cc_start: 0.5939 (mmp) cc_final: 0.3346 (mtp) REVERT: B 344 ARG cc_start: 0.6514 (ttt-90) cc_final: 0.6188 (ttt-90) REVERT: B 415 THR cc_start: 0.6291 (OUTLIER) cc_final: 0.5280 (p) REVERT: B 462 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8493 (t0) REVERT: B 737 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 875 MET cc_start: 0.7367 (tmm) cc_final: 0.6656 (tpp) REVERT: B 935 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7591 (p90) REVERT: B 961 MET cc_start: 0.8707 (ttm) cc_final: 0.8403 (ttm) REVERT: B 968 MET cc_start: 0.6834 (ttm) cc_final: 0.6456 (mtt) REVERT: B 991 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7083 (t0) REVERT: B 1020 ILE cc_start: 0.6188 (OUTLIER) cc_final: 0.5692 (mt) REVERT: B 1122 PRO cc_start: 0.7969 (Cg_exo) cc_final: 0.7702 (Cg_endo) REVERT: B 1142 MET cc_start: 0.8146 (ptm) cc_final: 0.7860 (ptm) REVERT: B 1146 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 1168 MET cc_start: 0.8619 (tpp) cc_final: 0.7633 (ttt) REVERT: B 1184 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6480 (mp0) outliers start: 101 outliers final: 82 residues processed: 284 average time/residue: 0.1456 time to fit residues: 66.2401 Evaluate side-chains 289 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 197 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 40 TRP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 877 THR Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1020 ILE Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 238 optimal weight: 1.9990 chunk 223 optimal weight: 0.3980 chunk 19 optimal weight: 0.0060 chunk 56 optimal weight: 0.0770 chunk 166 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 0.0370 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 361 HIS ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS ** B1124 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.162146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121368 restraints weight = 29708.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120076 restraints weight = 29664.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121633 restraints weight = 30123.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122528 restraints weight = 19479.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124091 restraints weight = 17303.307| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20691 Z= 0.119 Angle : 0.639 12.560 28243 Z= 0.305 Chirality : 0.041 0.220 3030 Planarity : 0.004 0.058 3603 Dihedral : 6.879 59.097 3421 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.75 % Allowed : 26.18 % Favored : 70.07 % 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: 0.38 (0.18), residues: 2396 helix: 1.36 (0.14), residues: 1495 sheet: -3.44 (1.55), residues: 10 loop : -1.68 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 942 TYR 0.020 0.001 TYR A1195 PHE 0.022 0.001 PHE A 343 TRP 0.022 0.001 TRP B 643 HIS 0.012 0.001 HIS B 963 Details of bonding type rmsd covalent geometry : bond 0.00258 (20644) covalent geometry : angle 0.62363 (28113) SS BOND : bond 0.00300 ( 11) SS BOND : angle 1.29778 ( 22) hydrogen bonds : bond 0.03528 ( 1056) hydrogen bonds : angle 4.05696 ( 3093) link_BETA1-4 : bond 0.00657 ( 16) link_BETA1-4 : angle 2.65427 ( 48) link_BETA1-6 : bond 0.00317 ( 1) link_BETA1-6 : angle 1.21951 ( 3) link_NAG-ASN : bond 0.00252 ( 19) link_NAG-ASN : angle 1.96573 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.95 seconds wall clock time: 50 minutes 15.54 seconds (3015.54 seconds total)