Starting phenix.real_space_refine on Sun Aug 24 13:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d5s_46581/08_2025/9d5s_46581.map" } resolution = 2.99 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= 0.016 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 12786 2.51 5 N 3371 2.21 5 O 3746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19989 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 9784 Classifications: {'peptide': 1201} Link IDs: {'PTRANS': 72, 'TRANS': 1128} Chain: "1" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9773 Classifications: {'peptide': 1199} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1126} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.87, per 1000 atoms: 0.24 Number of scatterers: 19989 At special positions: 0 Unit cell: (107.38, 137.942, 157.766, 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 3746 8.00 N 3371 7.00 C 12786 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 1 128 " - pdb=" SG CYS 1 136 " distance=2.04 Simple disulfide: pdb=" SG CYS 1 330 " - pdb=" SG CYS 1 348 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 516 " - pdb=" SG CYS 1 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 728 " - pdb=" SG CYS 1 734 " distance=2.04 Simple disulfide: pdb=" SG CYS 1 928 " - pdb=" SG CYS 1 946 " distance=2.03 Simple disulfide: pdb=" SG CYS 11114 " - pdb=" SG CYS 11126 " 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 648 " " NAG A1303 " - " ASN A 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 1 25 " " NAG P 1 " - " ASN 1 117 " " NAG Q 1 " - " ASN 1 289 " " NAG R 1 " - " ASN 1 416 " " NAG S 1 " - " ASN 1 480 " " NAG U 1 " - " ASN 1 685 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 963.9 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: 117 helices and 8 sheets defined 66.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.729A pdb=" N ASN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 77 Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.665A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.875A pdb=" N ASN A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 171 through 190 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.848A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 291 through 304 removed outlier: 3.511A pdb=" N ALA A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.629A 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: 3.978A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.697A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.561A pdb=" N LYS A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 4.114A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.557A pdb=" N CYS A 528 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.206A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 4.236A 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 606 through 610 Processing helix chain 'A' and resid 616 through 648 removed outlier: 4.004A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.207A pdb=" N ASP A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 724 Processing helix chain 'A' and resid 740 through 748 Processing helix chain 'A' and resid 750 through 770 Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 792 through 798 removed outlier: 3.711A 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 902 Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.101A pdb=" N ASN A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.845A 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: 3.716A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.834A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 3.982A pdb=" N ASP A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1068 removed outlier: 3.585A pdb=" N GLU A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1096 through 1118 removed outlier: 3.888A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A1118 " --> pdb=" O CYS A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 3.661A pdb=" N CYS A1126 " --> pdb=" O LEU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.869A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 4.351A pdb=" N ARG A1148 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1158 removed outlier: 3.704A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'A' and resid 1172 through 1187 Processing helix chain '1' and resid 13 through 42 removed outlier: 4.002A pdb=" N GLN 1 30 " --> pdb=" O SER 1 26 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 64 removed outlier: 4.432A pdb=" N GLN 1 54 " --> pdb=" O ASN 1 50 " (cutoff:3.500A) Processing helix chain '1' and resid 65 through 76 Processing helix chain '1' and resid 76 through 83 Processing helix chain '1' and resid 85 through 97 removed outlier: 3.681A pdb=" N THR 1 97 " --> pdb=" O GLY 1 93 " (cutoff:3.500A) Processing helix chain '1' and resid 104 through 124 Processing helix chain '1' and resid 141 through 150 Processing helix chain '1' and resid 152 through 169 Processing helix chain '1' and resid 171 through 190 Processing helix chain '1' and resid 193 through 201 removed outlier: 3.868A pdb=" N TRP 1 201 " --> pdb=" O TYR 1 197 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 238 Proline residue: 1 220 - end of helix Processing helix chain '1' and resid 261 through 268 removed outlier: 4.252A pdb=" N ASP 1 266 " --> pdb=" O ASN 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 286 Processing helix chain '1' and resid 291 through 304 removed outlier: 3.629A pdb=" N ARG 1 295 " --> pdb=" O THR 1 291 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU 1 304 " --> pdb=" O PHE 1 300 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 317 removed outlier: 4.008A pdb=" N GLU 1 315 " --> pdb=" O PRO 1 311 " (cutoff:3.500A) Processing helix chain '1' and resid 352 through 372 removed outlier: 3.874A pdb=" N TYR 1 372 " --> pdb=" O TYR 1 368 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 381 removed outlier: 4.416A pdb=" N ARG 1 381 " --> pdb=" O SER 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 401 removed outlier: 3.935A pdb=" N LEU 1 395 " --> pdb=" O ILE 1 391 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA 1 396 " --> pdb=" O GLY 1 392 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR 1 401 " --> pdb=" O LEU 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 408 Processing helix chain '1' and resid 417 through 433 removed outlier: 4.128A pdb=" N GLU 1 431 " --> pdb=" O LYS 1 427 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 451 removed outlier: 4.236A pdb=" N TYR 1 440 " --> pdb=" O LEU 1 436 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL 1 442 " --> pdb=" O PHE 1 438 " (cutoff:3.500A) Processing helix chain '1' and resid 455 through 457 No H-bonds generated for 'chain '1' and resid 455 through 457' Processing helix chain '1' and resid 458 through 470 Processing helix chain '1' and resid 484 through 488 Processing helix chain '1' and resid 498 through 518 removed outlier: 4.007A pdb=" N PHE 1 502 " --> pdb=" O TYR 1 498 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE 1 509 " --> pdb=" O PHE 1 505 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN 1 510 " --> pdb=" O VAL 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 546 removed outlier: 4.331A pdb=" N ALA 1 546 " --> pdb=" O LYS 1 542 " (cutoff:3.500A) Processing helix chain '1' and resid 551 through 560 removed outlier: 3.600A pdb=" N VAL 1 555 " --> pdb=" O PRO 1 551 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 574 Processing helix chain '1' and resid 574 through 589 Processing helix chain '1' and resid 616 through 648 removed outlier: 3.814A pdb=" N VAL 1 633 " --> pdb=" O ARG 1 629 " (cutoff:3.500A) Processing helix chain '1' and resid 653 through 677 removed outlier: 3.715A pdb=" N LYS 1 677 " --> pdb=" O THR 1 673 " (cutoff:3.500A) Processing helix chain '1' and resid 686 through 697 removed outlier: 4.039A pdb=" N ASP 1 697 " --> pdb=" O LYS 1 693 " (cutoff:3.500A) Processing helix chain '1' and resid 704 through 725 Processing helix chain '1' and resid 740 through 747 Processing helix chain '1' and resid 750 through 770 Processing helix chain '1' and resid 772 through 787 Processing helix chain '1' and resid 791 through 798 Processing helix chain '1' and resid 799 through 801 No H-bonds generated for 'chain '1' and resid 799 through 801' Processing helix chain '1' and resid 804 through 836 Proline residue: 1 818 - end of helix Processing helix chain '1' and resid 859 through 866 removed outlier: 3.520A pdb=" N ILE 1 862 " --> pdb=" O TRP 1 859 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP 1 864 " --> pdb=" O ASN 1 861 " (cutoff:3.500A) Processing helix chain '1' and resid 876 through 882 Processing helix chain '1' and resid 883 through 885 No H-bonds generated for 'chain '1' and resid 883 through 885' Processing helix chain '1' and resid 887 through 903 Processing helix chain '1' and resid 909 through 914 Processing helix chain '1' and resid 950 through 970 removed outlier: 3.724A pdb=" N LEU 1 954 " --> pdb=" O ASN 1 950 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR 1 970 " --> pdb=" O TYR 1 966 " (cutoff:3.500A) Processing helix chain '1' and resid 984 through 998 removed outlier: 4.551A pdb=" N GLY 1 990 " --> pdb=" O HIS 1 986 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP 1 991 " --> pdb=" O GLU 1 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU 1 993 " --> pdb=" O ILE 1 989 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER 1 996 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) Processing helix chain '1' and resid 999 through 1005 Processing helix chain '1' and resid 1015 through 1031 Processing helix chain '1' and resid 1032 through 1049 removed outlier: 4.617A pdb=" N PHE 11036 " --> pdb=" O ALA 11032 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP 11041 " --> pdb=" O SER 11037 " (cutoff:3.500A) Processing helix chain '1' and resid 1053 through 1055 No H-bonds generated for 'chain '1' and resid 1053 through 1055' Processing helix chain '1' and resid 1056 through 1068 removed outlier: 3.526A pdb=" N GLU 11060 " --> pdb=" O ASN 11056 " (cutoff:3.500A) Processing helix chain '1' and resid 1082 through 1087 Processing helix chain '1' and resid 1089 through 1093 removed outlier: 3.626A pdb=" N SER 11092 " --> pdb=" O HIS 11089 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER 11093 " --> pdb=" O ILE 11090 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1089 through 1093' Processing helix chain '1' and resid 1096 through 1117 removed outlier: 3.955A pdb=" N PHE 11100 " --> pdb=" O TYR 11096 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE 11107 " --> pdb=" O PHE 11103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN 11108 " --> pdb=" O ILE 11104 " (cutoff:3.500A) Processing helix chain '1' and resid 1131 through 1143 Processing helix chain '1' and resid 1149 through 1158 removed outlier: 3.920A pdb=" N ALA 11153 " --> pdb=" O PRO 11149 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1172 Processing helix chain '1' and resid 1172 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.166A 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 727 through 728 removed outlier: 3.554A pdb=" N VAL A 727 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.185A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '1' and resid 126 through 127 Processing sheet with id=AA5, first strand: chain '1' and resid 248 through 249 removed outlier: 6.258A pdb=" N ILE 1 248 " --> pdb=" O CYS 1 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '1' and resid 318 through 319 removed outlier: 7.107A pdb=" N MET 1 318 " --> pdb=" O GLN 1 347 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS 1 346 " --> pdb=" O SER 1 333 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER 1 333 " --> pdb=" O LYS 1 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '1' and resid 846 through 847 removed outlier: 6.422A pdb=" N ILE 1 846 " --> pdb=" O CYS 11072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '1' and resid 932 through 934 1068 hydrogen bonds defined for protein. 3111 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: 3.77 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6178 1.34 - 1.46: 4463 1.46 - 1.58: 9804 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 20589 Sorted by residual: bond pdb=" N LEU A 436 " pdb=" CA LEU A 436 " ideal model delta sigma weight residual 1.462 1.490 -0.029 9.50e-03 1.11e+04 9.16e+00 bond pdb=" N VAL 11040 " pdb=" CA VAL 11040 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.14e-02 7.69e+03 8.32e+00 bond pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.18e-02 7.18e+03 7.93e+00 bond pdb=" N ILE 11034 " pdb=" CA ILE 11034 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.23e-02 6.61e+03 7.86e+00 bond pdb=" N LEU A 441 " pdb=" CA LEU A 441 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.70e+00 ... (remaining 20584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 27481 2.00 - 4.01: 466 4.01 - 6.01: 80 6.01 - 8.01: 8 8.01 - 10.02: 3 Bond angle restraints: 28038 Sorted by residual: angle pdb=" CA TRP A 859 " pdb=" CB TRP A 859 " pdb=" CG TRP A 859 " ideal model delta sigma weight residual 113.60 120.43 -6.83 1.90e+00 2.77e-01 1.29e+01 angle pdb=" CA VAL 11040 " pdb=" C VAL 11040 " pdb=" O VAL 11040 " ideal model delta sigma weight residual 121.41 117.87 3.54 1.04e+00 9.25e-01 1.16e+01 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 133.96 -9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" CA VAL A 442 " pdb=" C VAL A 442 " pdb=" O VAL A 442 " ideal model delta sigma weight residual 121.29 117.97 3.32 1.07e+00 8.73e-01 9.63e+00 angle pdb=" CA LEU 11039 " pdb=" C LEU 11039 " pdb=" O LEU 11039 " ideal model delta sigma weight residual 120.82 117.70 3.12 1.05e+00 9.07e-01 8.83e+00 ... (remaining 28033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 10447 17.29 - 34.58: 1487 34.58 - 51.87: 457 51.87 - 69.15: 139 69.15 - 86.44: 30 Dihedral angle restraints: 12560 sinusoidal: 5506 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 -12.34 -73.66 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS 1 516 " pdb=" SG CYS 1 516 " pdb=" SG CYS 1 528 " pdb=" CB CYS 1 528 " ideal model delta sinusoidal sigma weight residual -86.00 -154.85 68.85 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS 1 330 " pdb=" SG CYS 1 330 " pdb=" SG CYS 1 348 " pdb=" CB CYS 1 348 " ideal model delta sinusoidal sigma weight residual -86.00 -154.30 68.30 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 12557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2355 0.048 - 0.096: 522 0.096 - 0.144: 114 0.144 - 0.192: 13 0.192 - 0.239: 6 Chirality restraints: 3010 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN 1 117 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 117 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 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 1.33e+00 ... (remaining 3007 not shown) Planarity restraints: 3614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 643 " 0.022 2.00e-02 2.50e+03 1.92e-02 9.25e+00 pdb=" CG TRP A 643 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 643 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 643 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 643 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 643 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 643 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 643 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 643 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 68 " -0.017 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP A 68 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 68 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 68 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 68 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 68 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 68 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 68 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 68 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 64 " -0.009 2.00e-02 2.50e+03 1.43e-02 3.56e+00 pdb=" CG PHE A 64 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 64 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 64 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 64 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 64 " 0.000 2.00e-02 2.50e+03 ... (remaining 3611 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3787 2.77 - 3.30: 19463 3.30 - 3.83: 34991 3.83 - 4.37: 39261 4.37 - 4.90: 68923 Nonbonded interactions: 166425 Sorted by model distance: nonbonded pdb=" OG SER 1 996 " pdb=" OD1 ASP 11127 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU 1 299 " pdb=" OH TYR 1 531 " model vdw 2.234 3.040 nonbonded pdb=" O LEU A 375 " pdb=" NH2 ARG A 380 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR 1 820 " pdb=" O GLN 11069 " model vdw 2.250 3.040 nonbonded pdb=" O TYR A 202 " pdb=" NE1 TRP A 552 " model vdw 2.253 3.120 ... (remaining 166420 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 '1' selection = (chain 'A' and resid 2 through 1200) } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.010 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 20632 Z= 0.181 Angle : 0.648 10.015 28156 Z= 0.328 Chirality : 0.043 0.239 3010 Planarity : 0.004 0.044 3599 Dihedral : 18.075 86.442 7983 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.18 % Allowed : 27.13 % Favored : 68.69 % 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: 0.30 (0.18), residues: 2396 helix: 1.33 (0.14), residues: 1474 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 344 TYR 0.017 0.001 TYR 1 607 PHE 0.030 0.001 PHE A 64 TRP 0.053 0.002 TRP A 643 HIS 0.005 0.001 HIS 1 226 Details of bonding type rmsd covalent geometry : bond 0.00376 (20589) covalent geometry : angle 0.62040 (28038) SS BOND : bond 0.00326 ( 11) SS BOND : angle 1.80035 ( 22) hydrogen bonds : bond 0.13211 ( 1068) hydrogen bonds : angle 5.23516 ( 3111) link_BETA1-4 : bond 0.00807 ( 16) link_BETA1-4 : angle 3.43278 ( 48) link_BETA1-6 : bond 0.00034 ( 1) link_BETA1-6 : angle 1.53650 ( 3) link_NAG-ASN : bond 0.00511 ( 15) link_NAG-ASN : angle 2.97477 ( 45) *********************** 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 278 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7761 (mp10) cc_final: 0.7556 (mp10) REVERT: A 60 LEU cc_start: 0.7756 (pp) cc_final: 0.7251 (tm) REVERT: A 62 GLN cc_start: 0.8130 (tp40) cc_final: 0.7929 (tm-30) REVERT: A 63 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 88 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6833 (tt) REVERT: A 203 ASN cc_start: 0.7793 (t0) cc_final: 0.6994 (p0) REVERT: A 306 LEU cc_start: 0.3589 (OUTLIER) cc_final: 0.3112 (mp) REVERT: A 355 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5471 (mp10) REVERT: A 626 GLU cc_start: 0.7149 (tt0) cc_final: 0.6842 (tp30) REVERT: A 707 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7342 (mt-10) REVERT: A 709 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7219 (tp30) REVERT: A 859 TRP cc_start: 0.8256 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 891 MET cc_start: 0.6760 (mtp) cc_final: 0.6460 (mtt) REVERT: A 897 ASP cc_start: 0.8054 (t0) cc_final: 0.7786 (m-30) REVERT: A 1124 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6572 (p90) REVERT: A 1143 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8248 (mtpt) REVERT: 1 283 MET cc_start: 0.5662 (mtt) cc_final: 0.4454 (mpm) REVERT: 1 374 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.6551 (t70) REVERT: 1 391 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8027 (mp) REVERT: 1 518 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: 1 637 GLU cc_start: 0.6946 (tt0) cc_final: 0.6521 (mm-30) REVERT: 1 743 ASN cc_start: 0.8382 (t0) cc_final: 0.8019 (t0) REVERT: 1 875 MET cc_start: 0.4217 (OUTLIER) cc_final: 0.3997 (mtm) REVERT: 1 1053 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8582 (p) REVERT: 1 1098 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8331 (ptm160) outliers start: 87 outliers final: 51 residues processed: 255 average time/residue: 0.5390 time to fit residues: 159.9328 Evaluate side-chains 236 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 114 LEU Chi-restraints excluded: chain 1 residue 147 LEU Chi-restraints excluded: chain 1 residue 181 LEU Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 374 ASP Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 540 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 612 ASP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 753 ASP Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 875 MET Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.2980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 367 GLN ** 1 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11007 ASN 11058 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.170398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111496 restraints weight = 26529.687| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.77 r_work: 0.3250 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20632 Z= 0.168 Angle : 0.657 10.200 28156 Z= 0.317 Chirality : 0.043 0.248 3010 Planarity : 0.004 0.046 3599 Dihedral : 8.968 59.034 3398 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.69 % Allowed : 25.20 % Favored : 68.11 % 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: 0.35 (0.18), residues: 2396 helix: 1.36 (0.14), residues: 1490 sheet: None (None), residues: 0 loop : -1.75 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 344 TYR 0.015 0.002 TYR A 645 PHE 0.014 0.001 PHE A 64 TRP 0.031 0.001 TRP A 643 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00392 (20589) covalent geometry : angle 0.63018 (28038) SS BOND : bond 0.00312 ( 11) SS BOND : angle 1.30323 ( 22) hydrogen bonds : bond 0.04699 ( 1068) hydrogen bonds : angle 4.39470 ( 3111) link_BETA1-4 : bond 0.00765 ( 16) link_BETA1-4 : angle 3.40992 ( 48) link_BETA1-6 : bond 0.00106 ( 1) link_BETA1-6 : angle 1.78730 ( 3) link_NAG-ASN : bond 0.00483 ( 15) link_NAG-ASN : angle 3.07549 ( 45) *********************** 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 328 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 189 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7751 (mp10) cc_final: 0.7532 (mp10) REVERT: A 60 LEU cc_start: 0.7636 (pp) cc_final: 0.7155 (tm) REVERT: A 62 GLN cc_start: 0.8117 (tp40) cc_final: 0.7886 (tm-30) REVERT: A 63 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 66 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 68 TRP cc_start: 0.7464 (m100) cc_final: 0.7263 (m100) REVERT: A 88 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6942 (tt) REVERT: A 203 ASN cc_start: 0.8044 (t0) cc_final: 0.7239 (p0) REVERT: A 352 THR cc_start: 0.3932 (OUTLIER) cc_final: 0.3051 (m) REVERT: A 355 GLN cc_start: 0.5922 (OUTLIER) cc_final: 0.5164 (mp10) REVERT: A 393 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (t0) REVERT: A 707 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7331 (mt-10) REVERT: A 709 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7130 (tp30) REVERT: A 859 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.7510 (p90) REVERT: A 897 ASP cc_start: 0.8072 (t0) cc_final: 0.7746 (m-30) REVERT: A 918 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 989 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6958 (mt) REVERT: A 1124 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6490 (p90) REVERT: A 1143 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8090 (mtpt) REVERT: 1 147 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8179 (mp) REVERT: 1 283 MET cc_start: 0.5735 (mtt) cc_final: 0.4557 (mpt) REVERT: 1 353 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7664 (ttp) REVERT: 1 367 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: 1 374 ASP cc_start: 0.7906 (m-30) cc_final: 0.6738 (t70) REVERT: 1 391 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7931 (mp) REVERT: 1 418 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6699 (t) REVERT: 1 518 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: 1 559 MET cc_start: 0.7821 (ttt) cc_final: 0.7573 (ttt) REVERT: 1 637 GLU cc_start: 0.6801 (tt0) cc_final: 0.6371 (mm-30) REVERT: 1 677 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.5901 (pttm) REVERT: 1 699 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: 1 743 ASN cc_start: 0.8189 (t0) cc_final: 0.7775 (t0) REVERT: 1 1053 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8497 (p) outliers start: 139 outliers final: 60 residues processed: 296 average time/residue: 0.5442 time to fit residues: 187.0239 Evaluate side-chains 252 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 147 LEU Chi-restraints excluded: chain 1 residue 181 LEU Chi-restraints excluded: chain 1 residue 264 ILE Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 353 MET Chi-restraints excluded: chain 1 residue 367 GLN Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 418 THR Chi-restraints excluded: chain 1 residue 428 MET Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 540 LEU Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 698 LEU Chi-restraints excluded: chain 1 residue 699 GLU Chi-restraints excluded: chain 1 residue 717 ASP Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 935 PHE Chi-restraints excluded: chain 1 residue 997 VAL Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 184 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 229 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 HIS 1 251 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 661 ASN ** 1 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11007 ASN 11058 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.169303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110270 restraints weight = 26573.772| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.79 r_work: 0.3236 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20632 Z= 0.189 Angle : 0.667 11.429 28156 Z= 0.321 Chirality : 0.044 0.243 3010 Planarity : 0.005 0.048 3599 Dihedral : 8.690 58.729 3356 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 7.36 % Allowed : 24.48 % Favored : 68.16 % 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: 0.33 (0.18), residues: 2396 helix: 1.36 (0.13), residues: 1480 sheet: -3.83 (1.20), residues: 12 loop : -1.71 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 381 TYR 0.020 0.002 TYR A 645 PHE 0.014 0.001 PHE A 502 TRP 0.038 0.002 TRP A 643 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00452 (20589) covalent geometry : angle 0.64058 (28038) SS BOND : bond 0.00534 ( 11) SS BOND : angle 1.48127 ( 22) hydrogen bonds : bond 0.04668 ( 1068) hydrogen bonds : angle 4.30208 ( 3111) link_BETA1-4 : bond 0.00805 ( 16) link_BETA1-4 : angle 3.39348 ( 48) link_BETA1-6 : bond 0.00108 ( 1) link_BETA1-6 : angle 1.86419 ( 3) link_NAG-ASN : bond 0.00491 ( 15) link_NAG-ASN : angle 3.04255 ( 45) *********************** 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 341 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 188 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7850 (mp10) cc_final: 0.7626 (mp10) REVERT: A 60 LEU cc_start: 0.7619 (pp) cc_final: 0.7157 (tm) REVERT: A 62 GLN cc_start: 0.8120 (tp40) cc_final: 0.7817 (tm-30) REVERT: A 63 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 66 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 68 TRP cc_start: 0.7500 (m100) cc_final: 0.6965 (m100) REVERT: A 108 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6098 (ttt90) REVERT: A 177 ASP cc_start: 0.7552 (m-30) cc_final: 0.7335 (m-30) REVERT: A 203 ASN cc_start: 0.8075 (t0) cc_final: 0.7254 (p0) REVERT: A 306 LEU cc_start: 0.3709 (OUTLIER) cc_final: 0.3175 (mp) REVERT: A 352 THR cc_start: 0.4046 (OUTLIER) cc_final: 0.2899 (m) REVERT: A 353 MET cc_start: 0.6266 (tpt) cc_final: 0.5651 (pmt) REVERT: A 355 GLN cc_start: 0.5855 (tm-30) cc_final: 0.5091 (mp10) REVERT: A 393 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7550 (t0) REVERT: A 431 GLU cc_start: 0.8579 (tt0) cc_final: 0.8266 (tt0) REVERT: A 613 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 707 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7307 (mt-10) REVERT: A 709 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7160 (tp30) REVERT: A 763 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: A 859 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.7450 (p90) REVERT: A 897 ASP cc_start: 0.8052 (t0) cc_final: 0.7712 (m-30) REVERT: A 918 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 989 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6871 (mt) REVERT: A 997 VAL cc_start: 0.6320 (p) cc_final: 0.5990 (m) REVERT: A 1119 HIS cc_start: 0.4779 (OUTLIER) cc_final: 0.3168 (t-90) REVERT: A 1124 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6481 (p90) REVERT: A 1143 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8054 (mtpt) REVERT: 1 147 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8178 (mp) REVERT: 1 219 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: 1 283 MET cc_start: 0.5674 (mtt) cc_final: 0.4591 (mpt) REVERT: 1 374 ASP cc_start: 0.7952 (m-30) cc_final: 0.6743 (t70) REVERT: 1 391 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7919 (mp) REVERT: 1 418 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6717 (t) REVERT: 1 518 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: 1 521 TYR cc_start: 0.6074 (t80) cc_final: 0.5786 (t80) REVERT: 1 559 MET cc_start: 0.7758 (ttt) cc_final: 0.7552 (ttt) REVERT: 1 590 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6492 (pt0) REVERT: 1 637 GLU cc_start: 0.6884 (tt0) cc_final: 0.6435 (mm-30) REVERT: 1 677 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.5872 (pttm) REVERT: 1 699 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: 1 743 ASN cc_start: 0.8218 (t0) cc_final: 0.7810 (t0) REVERT: 1 1029 ASP cc_start: 0.8532 (m-30) cc_final: 0.8196 (m-30) REVERT: 1 1053 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8511 (p) outliers start: 153 outliers final: 80 residues processed: 311 average time/residue: 0.4962 time to fit residues: 181.9564 Evaluate side-chains 276 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 176 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 986 HIS Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 147 LEU Chi-restraints excluded: chain 1 residue 181 LEU Chi-restraints excluded: chain 1 residue 219 GLU Chi-restraints excluded: chain 1 residue 256 MET Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 330 CYS Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 418 THR Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 453 ARG Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 540 LEU Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 590 GLU Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 657 LEU Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 680 VAL Chi-restraints excluded: chain 1 residue 698 LEU Chi-restraints excluded: chain 1 residue 699 GLU Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 953 ASP Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1023 LEU Chi-restraints excluded: chain 1 residue 1031 ILE Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1058 ASN Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 149 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 491 HIS ** 1 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11058 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.171618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112916 restraints weight = 26682.393| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.80 r_work: 0.3270 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20632 Z= 0.131 Angle : 0.626 9.813 28156 Z= 0.298 Chirality : 0.041 0.245 3010 Planarity : 0.004 0.046 3599 Dihedral : 8.340 58.188 3350 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.40 % Allowed : 25.54 % Favored : 68.06 % 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: 0.44 (0.18), residues: 2396 helix: 1.45 (0.13), residues: 1485 sheet: -4.05 (1.05), residues: 12 loop : -1.68 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.017 0.001 TYR A 645 PHE 0.012 0.001 PHE A 502 TRP 0.022 0.001 TRP A 643 HIS 0.004 0.001 HIS 1 226 Details of bonding type rmsd covalent geometry : bond 0.00295 (20589) covalent geometry : angle 0.59898 (28038) SS BOND : bond 0.00346 ( 11) SS BOND : angle 1.48680 ( 22) hydrogen bonds : bond 0.04085 ( 1068) hydrogen bonds : angle 4.17367 ( 3111) link_BETA1-4 : bond 0.00802 ( 16) link_BETA1-4 : angle 3.31401 ( 48) link_BETA1-6 : bond 0.00038 ( 1) link_BETA1-6 : angle 1.91888 ( 3) link_NAG-ASN : bond 0.00618 ( 15) link_NAG-ASN : angle 2.91989 ( 45) *********************** 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 319 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 186 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7862 (mp10) cc_final: 0.7629 (mp10) REVERT: A 60 LEU cc_start: 0.7598 (pp) cc_final: 0.7117 (tm) REVERT: A 62 GLN cc_start: 0.8102 (tp40) cc_final: 0.7839 (tm-30) REVERT: A 63 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 68 TRP cc_start: 0.7510 (m100) cc_final: 0.6944 (m100) REVERT: A 88 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6889 (tt) REVERT: A 177 ASP cc_start: 0.7530 (m-30) cc_final: 0.7298 (m-30) REVERT: A 203 ASN cc_start: 0.8045 (t0) cc_final: 0.7250 (p0) REVERT: A 352 THR cc_start: 0.3960 (OUTLIER) cc_final: 0.2752 (m) REVERT: A 353 MET cc_start: 0.6161 (tpt) cc_final: 0.5578 (pmt) REVERT: A 355 GLN cc_start: 0.5825 (tm-30) cc_final: 0.5076 (mp10) REVERT: A 431 GLU cc_start: 0.8523 (tt0) cc_final: 0.8260 (tt0) REVERT: A 707 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7305 (mt-10) REVERT: A 709 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7091 (tp30) REVERT: A 763 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6227 (m-30) REVERT: A 859 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.7596 (p90) REVERT: A 897 ASP cc_start: 0.8029 (t0) cc_final: 0.7684 (m-30) REVERT: A 989 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6806 (mt) REVERT: A 997 VAL cc_start: 0.6295 (p) cc_final: 0.5903 (m) REVERT: A 1124 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6393 (p90) REVERT: A 1143 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8130 (mtpt) REVERT: 1 219 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: 1 283 MET cc_start: 0.5487 (mtt) cc_final: 0.4557 (mpt) REVERT: 1 293 MET cc_start: 0.6296 (pmm) cc_final: 0.5760 (pmm) REVERT: 1 374 ASP cc_start: 0.7885 (m-30) cc_final: 0.6674 (t70) REVERT: 1 391 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7941 (mp) REVERT: 1 518 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: 1 559 MET cc_start: 0.7699 (ttt) cc_final: 0.7496 (ttt) REVERT: 1 637 GLU cc_start: 0.6872 (tt0) cc_final: 0.6418 (mm-30) REVERT: 1 677 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.5799 (pttm) REVERT: 1 699 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: 1 743 ASN cc_start: 0.8167 (t0) cc_final: 0.7742 (t0) REVERT: 1 1053 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8433 (p) outliers start: 133 outliers final: 67 residues processed: 289 average time/residue: 0.5188 time to fit residues: 176.7412 Evaluate side-chains 258 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 179 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU 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 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 219 GLU Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 353 MET Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 540 LEU Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 657 LEU Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 699 GLU Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 953 ASP Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1031 ILE Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1058 ASN Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 197 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 85 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** 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 = 0.4134 r_free = 0.4134 target = 0.171801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113065 restraints weight = 26403.870| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.41 r_work: 0.3294 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20632 Z= 0.130 Angle : 0.622 9.639 28156 Z= 0.296 Chirality : 0.041 0.243 3010 Planarity : 0.004 0.045 3599 Dihedral : 8.163 58.414 3342 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.78 % Allowed : 25.20 % Favored : 68.01 % 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: 0.52 (0.18), residues: 2396 helix: 1.53 (0.13), residues: 1483 sheet: -4.13 (1.02), residues: 12 loop : -1.67 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.017 0.001 TYR A 645 PHE 0.015 0.001 PHE 1 64 TRP 0.032 0.001 TRP A 643 HIS 0.004 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00296 (20589) covalent geometry : angle 0.59533 (28038) SS BOND : bond 0.00354 ( 11) SS BOND : angle 1.52726 ( 22) hydrogen bonds : bond 0.04009 ( 1068) hydrogen bonds : angle 4.11930 ( 3111) link_BETA1-4 : bond 0.00833 ( 16) link_BETA1-4 : angle 3.26036 ( 48) link_BETA1-6 : bond 0.00073 ( 1) link_BETA1-6 : angle 1.89901 ( 3) link_NAG-ASN : bond 0.00576 ( 15) link_NAG-ASN : angle 2.87065 ( 45) *********************** 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 334 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 193 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7895 (mp10) cc_final: 0.7655 (mp10) REVERT: A 60 LEU cc_start: 0.7614 (pp) cc_final: 0.7099 (tm) REVERT: A 62 GLN cc_start: 0.8144 (tp40) cc_final: 0.7811 (tm-30) REVERT: A 63 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 66 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 68 TRP cc_start: 0.7564 (m100) cc_final: 0.7027 (m100) REVERT: A 88 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6921 (tt) REVERT: A 108 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6053 (ttt90) REVERT: A 177 ASP cc_start: 0.7484 (m-30) cc_final: 0.7236 (m-30) REVERT: A 203 ASN cc_start: 0.8043 (t0) cc_final: 0.7334 (p0) REVERT: A 352 THR cc_start: 0.4082 (OUTLIER) cc_final: 0.2891 (m) REVERT: A 353 MET cc_start: 0.6139 (tpt) cc_final: 0.5599 (pmt) REVERT: A 355 GLN cc_start: 0.5829 (tm-30) cc_final: 0.5074 (mp10) REVERT: A 393 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 431 GLU cc_start: 0.8532 (tt0) cc_final: 0.8250 (tt0) REVERT: A 613 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 707 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7305 (mt-10) REVERT: A 709 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7061 (tp30) REVERT: A 763 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: A 859 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.7638 (p90) REVERT: A 897 ASP cc_start: 0.8030 (t0) cc_final: 0.7689 (m-30) REVERT: A 918 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 989 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6892 (mt) REVERT: A 997 VAL cc_start: 0.6522 (p) cc_final: 0.6195 (m) REVERT: A 1119 HIS cc_start: 0.4673 (OUTLIER) cc_final: 0.3094 (t-90) REVERT: A 1124 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6369 (p90) REVERT: A 1143 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8049 (mtmt) REVERT: 1 219 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: 1 283 MET cc_start: 0.5394 (mtt) cc_final: 0.4551 (mpt) REVERT: 1 293 MET cc_start: 0.6279 (pmm) cc_final: 0.5727 (pmm) REVERT: 1 374 ASP cc_start: 0.7864 (m-30) cc_final: 0.6661 (t70) REVERT: 1 391 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7933 (mp) REVERT: 1 518 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: 1 637 GLU cc_start: 0.6894 (tt0) cc_final: 0.6660 (mm-30) REVERT: 1 677 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.5839 (pttm) REVERT: 1 699 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: 1 743 ASN cc_start: 0.8136 (t0) cc_final: 0.7748 (t0) REVERT: 1 875 MET cc_start: 0.3612 (OUTLIER) cc_final: 0.2994 (mtm) REVERT: 1 1053 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8433 (p) REVERT: 1 1152 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6322 (mp0) outliers start: 141 outliers final: 79 residues processed: 304 average time/residue: 0.4987 time to fit residues: 178.0844 Evaluate side-chains 273 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 176 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 219 GLU Chi-restraints excluded: chain 1 residue 264 ILE Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 540 LEU Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 657 LEU Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 699 GLU Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 875 MET Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1023 LEU Chi-restraints excluded: chain 1 residue 1031 ILE Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 128 optimal weight: 0.4980 chunk 148 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 582 GLN 1 950 ASN ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11058 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114540 restraints weight = 26404.710| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.41 r_work: 0.3316 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20632 Z= 0.117 Angle : 0.612 9.355 28156 Z= 0.290 Chirality : 0.041 0.244 3010 Planarity : 0.004 0.044 3599 Dihedral : 8.016 59.409 3340 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.25 % Allowed : 25.97 % Favored : 67.77 % 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: 0.61 (0.18), residues: 2396 helix: 1.59 (0.13), residues: 1484 sheet: -4.22 (0.98), residues: 12 loop : -1.63 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 11148 TYR 0.017 0.001 TYR A 645 PHE 0.017 0.001 PHE 1 64 TRP 0.036 0.001 TRP A 643 HIS 0.003 0.001 HIS 1 164 Details of bonding type rmsd covalent geometry : bond 0.00254 (20589) covalent geometry : angle 0.58715 (28038) SS BOND : bond 0.00600 ( 11) SS BOND : angle 1.49333 ( 22) hydrogen bonds : bond 0.03755 ( 1068) hydrogen bonds : angle 4.05780 ( 3111) link_BETA1-4 : bond 0.00797 ( 16) link_BETA1-4 : angle 3.18558 ( 48) link_BETA1-6 : bond 0.00098 ( 1) link_BETA1-6 : angle 1.88811 ( 3) link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 2.78595 ( 45) *********************** 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 318 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 188 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7906 (mp10) cc_final: 0.7664 (mp10) REVERT: A 60 LEU cc_start: 0.7607 (pp) cc_final: 0.7062 (tm) REVERT: A 62 GLN cc_start: 0.8118 (tp40) cc_final: 0.7835 (tm-30) REVERT: A 63 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 68 TRP cc_start: 0.7558 (m100) cc_final: 0.7098 (m100) REVERT: A 88 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6986 (tt) REVERT: A 177 ASP cc_start: 0.7539 (m-30) cc_final: 0.7293 (m-30) REVERT: A 203 ASN cc_start: 0.8048 (t0) cc_final: 0.7392 (p0) REVERT: A 273 ASP cc_start: 0.7261 (p0) cc_final: 0.7055 (m-30) REVERT: A 306 LEU cc_start: 0.3837 (OUTLIER) cc_final: 0.3187 (mp) REVERT: A 352 THR cc_start: 0.4116 (OUTLIER) cc_final: 0.2915 (m) REVERT: A 353 MET cc_start: 0.6184 (tpt) cc_final: 0.5681 (pmt) REVERT: A 355 GLN cc_start: 0.5852 (tm-30) cc_final: 0.5084 (mp10) REVERT: A 393 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7610 (t0) REVERT: A 431 GLU cc_start: 0.8529 (tt0) cc_final: 0.8255 (tt0) REVERT: A 707 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7308 (mt-10) REVERT: A 763 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: A 859 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7663 (p90) REVERT: A 897 ASP cc_start: 0.8032 (t0) cc_final: 0.7689 (m-30) REVERT: A 918 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 989 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6913 (mt) REVERT: A 997 VAL cc_start: 0.6499 (p) cc_final: 0.6100 (m) REVERT: A 1124 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6306 (p90) REVERT: A 1143 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8053 (mtmt) REVERT: 1 283 MET cc_start: 0.5409 (mtt) cc_final: 0.4606 (mpt) REVERT: 1 293 MET cc_start: 0.6244 (pmm) cc_final: 0.5717 (pmm) REVERT: 1 374 ASP cc_start: 0.7828 (m-30) cc_final: 0.6677 (t70) REVERT: 1 391 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (mp) REVERT: 1 592 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6201 (tp) REVERT: 1 677 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.5811 (pttm) REVERT: 1 709 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7393 (mm-30) REVERT: 1 743 ASN cc_start: 0.8187 (t0) cc_final: 0.7808 (t0) REVERT: 1 1053 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8352 (p) outliers start: 130 outliers final: 67 residues processed: 288 average time/residue: 0.5133 time to fit residues: 173.9461 Evaluate side-chains 258 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 178 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 105 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 657 LEU Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 680 VAL Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1023 LEU Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1102 SER Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 105 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** 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 = 0.4153 r_free = 0.4153 target = 0.173605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115250 restraints weight = 26494.039| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.75 r_work: 0.3309 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20632 Z= 0.117 Angle : 0.612 9.362 28156 Z= 0.291 Chirality : 0.041 0.243 3010 Planarity : 0.004 0.044 3599 Dihedral : 7.773 59.680 3332 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.92 % Allowed : 26.55 % Favored : 67.53 % 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: 0.72 (0.18), residues: 2396 helix: 1.70 (0.13), residues: 1478 sheet: -4.16 (1.01), residues: 12 loop : -1.59 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11148 TYR 0.018 0.001 TYR A 645 PHE 0.013 0.001 PHE 1 64 TRP 0.026 0.001 TRP 1 40 HIS 0.003 0.001 HIS 1 164 Details of bonding type rmsd covalent geometry : bond 0.00256 (20589) covalent geometry : angle 0.58693 (28038) SS BOND : bond 0.00354 ( 11) SS BOND : angle 1.49607 ( 22) hydrogen bonds : bond 0.03710 ( 1068) hydrogen bonds : angle 4.03149 ( 3111) link_BETA1-4 : bond 0.00783 ( 16) link_BETA1-4 : angle 3.14420 ( 48) link_BETA1-6 : bond 0.00003 ( 1) link_BETA1-6 : angle 1.82458 ( 3) link_NAG-ASN : bond 0.00613 ( 15) link_NAG-ASN : angle 2.73959 ( 45) *********************** 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 310 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 187 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7882 (mt0) cc_final: 0.7634 (mp10) REVERT: A 60 LEU cc_start: 0.7566 (pp) cc_final: 0.7011 (tm) REVERT: A 62 GLN cc_start: 0.8095 (tp40) cc_final: 0.7815 (tm-30) REVERT: A 63 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 68 TRP cc_start: 0.7526 (m100) cc_final: 0.7016 (m100) REVERT: A 88 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6977 (tt) REVERT: A 203 ASN cc_start: 0.8076 (t0) cc_final: 0.7437 (p0) REVERT: A 293 MET cc_start: 0.5246 (mpp) cc_final: 0.4748 (ptt) REVERT: A 306 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3262 (mp) REVERT: A 352 THR cc_start: 0.4031 (OUTLIER) cc_final: 0.2842 (m) REVERT: A 353 MET cc_start: 0.6181 (tpt) cc_final: 0.5693 (pmt) REVERT: A 355 GLN cc_start: 0.5823 (tm-30) cc_final: 0.5005 (mp10) REVERT: A 393 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 431 GLU cc_start: 0.8552 (tt0) cc_final: 0.8265 (tt0) REVERT: A 707 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7284 (mt-10) REVERT: A 763 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6210 (m-30) REVERT: A 859 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.7689 (p90) REVERT: A 897 ASP cc_start: 0.8063 (t0) cc_final: 0.7685 (m-30) REVERT: A 916 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.5588 (tmm) REVERT: A 989 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6866 (mt) REVERT: A 997 VAL cc_start: 0.6477 (p) cc_final: 0.6164 (m) REVERT: A 1119 HIS cc_start: 0.4672 (OUTLIER) cc_final: 0.3074 (t-90) REVERT: A 1143 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7990 (mtmt) REVERT: 1 145 ASN cc_start: 0.8449 (m-40) cc_final: 0.8242 (m-40) REVERT: 1 283 MET cc_start: 0.5285 (mtt) cc_final: 0.4513 (mpt) REVERT: 1 293 MET cc_start: 0.6187 (pmm) cc_final: 0.5662 (pmm) REVERT: 1 348 CYS cc_start: 0.3108 (m) cc_final: 0.1873 (p) REVERT: 1 374 ASP cc_start: 0.7828 (m-30) cc_final: 0.6728 (t70) REVERT: 1 391 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7882 (mp) REVERT: 1 518 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: 1 592 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6227 (tp) REVERT: 1 625 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6739 (tm-30) REVERT: 1 660 LYS cc_start: 0.5700 (OUTLIER) cc_final: 0.5431 (mmmm) REVERT: 1 677 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.5792 (pttm) REVERT: 1 743 ASN cc_start: 0.8179 (t0) cc_final: 0.7775 (t0) outliers start: 123 outliers final: 72 residues processed: 285 average time/residue: 0.4307 time to fit residues: 145.3973 Evaluate side-chains 260 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 174 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LYS 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 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 105 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 660 LYS Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 680 VAL Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1023 LEU Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1102 SER Chi-restraints excluded: chain 1 residue 1105 ILE Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 chunk 185 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 950 ASN A1124 HIS A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** 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 = 0.4150 r_free = 0.4150 target = 0.173253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118088 restraints weight = 26421.224| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.86 r_work: 0.3299 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20632 Z= 0.122 Angle : 0.616 9.363 28156 Z= 0.293 Chirality : 0.041 0.243 3010 Planarity : 0.004 0.043 3599 Dihedral : 7.603 59.898 3323 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.48 % Allowed : 27.08 % Favored : 67.44 % 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: 0.70 (0.18), residues: 2396 helix: 1.66 (0.13), residues: 1492 sheet: -3.86 (0.79), residues: 22 loop : -1.58 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 11148 TYR 0.017 0.001 TYR A 372 PHE 0.013 0.001 PHE 1 20 TRP 0.029 0.001 TRP A 643 HIS 0.009 0.001 HIS A1124 Details of bonding type rmsd covalent geometry : bond 0.00274 (20589) covalent geometry : angle 0.59173 (28038) SS BOND : bond 0.00335 ( 11) SS BOND : angle 1.59890 ( 22) hydrogen bonds : bond 0.03737 ( 1068) hydrogen bonds : angle 4.02349 ( 3111) link_BETA1-4 : bond 0.00794 ( 16) link_BETA1-4 : angle 3.10254 ( 48) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 1.82281 ( 3) link_NAG-ASN : bond 0.00496 ( 15) link_NAG-ASN : angle 2.70816 ( 45) *********************** 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 296 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 182 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7870 (mt0) cc_final: 0.7615 (mp10) REVERT: A 60 LEU cc_start: 0.7598 (pp) cc_final: 0.7014 (tm) REVERT: A 62 GLN cc_start: 0.8131 (tp40) cc_final: 0.7784 (tm-30) REVERT: A 63 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 66 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 68 TRP cc_start: 0.7558 (m100) cc_final: 0.7141 (m100) REVERT: A 88 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6985 (tt) REVERT: A 108 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5909 (ttt90) REVERT: A 203 ASN cc_start: 0.7919 (t0) cc_final: 0.7335 (p0) REVERT: A 293 MET cc_start: 0.5057 (mpp) cc_final: 0.4647 (ptt) REVERT: A 306 LEU cc_start: 0.3868 (OUTLIER) cc_final: 0.3276 (mp) REVERT: A 352 THR cc_start: 0.4148 (OUTLIER) cc_final: 0.3008 (m) REVERT: A 353 MET cc_start: 0.6123 (tpt) cc_final: 0.5669 (pmt) REVERT: A 355 GLN cc_start: 0.5822 (tm-30) cc_final: 0.5002 (mp10) REVERT: A 393 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7427 (t0) REVERT: A 431 GLU cc_start: 0.8375 (tt0) cc_final: 0.8094 (tt0) REVERT: A 707 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7117 (mt-10) REVERT: A 763 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6178 (m-30) REVERT: A 859 TRP cc_start: 0.8390 (OUTLIER) cc_final: 0.7585 (p90) REVERT: A 862 ILE cc_start: 0.3769 (OUTLIER) cc_final: 0.2957 (tp) REVERT: A 897 ASP cc_start: 0.8051 (t0) cc_final: 0.7672 (m-30) REVERT: A 989 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6778 (mt) REVERT: A 1119 HIS cc_start: 0.4502 (OUTLIER) cc_final: 0.3036 (t-90) REVERT: A 1124 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6294 (p90) REVERT: A 1143 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8059 (mtmt) REVERT: 1 145 ASN cc_start: 0.8427 (m-40) cc_final: 0.8215 (m-40) REVERT: 1 283 MET cc_start: 0.5340 (mtt) cc_final: 0.4586 (mpt) REVERT: 1 293 MET cc_start: 0.6143 (pmm) cc_final: 0.5570 (pmm) REVERT: 1 348 CYS cc_start: 0.2883 (m) cc_final: 0.1762 (p) REVERT: 1 374 ASP cc_start: 0.7770 (m-30) cc_final: 0.6727 (t70) REVERT: 1 391 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7832 (mp) REVERT: 1 518 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: 1 592 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.6051 (tp) REVERT: 1 677 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.5779 (pttm) REVERT: 1 709 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7293 (mm-30) REVERT: 1 743 ASN cc_start: 0.8147 (t0) cc_final: 0.7802 (t0) REVERT: 1 744 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7907 (p) REVERT: 1 875 MET cc_start: 0.2326 (mmt) cc_final: 0.2115 (mmt) outliers start: 114 outliers final: 77 residues processed: 274 average time/residue: 0.4377 time to fit residues: 142.1639 Evaluate side-chains 266 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 173 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 114 LEU 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 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 518 GLU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 680 VAL Chi-restraints excluded: chain 1 residue 729 HIS Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 935 PHE Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1102 SER Chi-restraints excluded: chain 1 residue 1105 ILE Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 210 optimal weight: 0.6980 chunk 196 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN A 950 ASN A1124 HIS A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119110 restraints weight = 26239.658| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.85 r_work: 0.3297 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20632 Z= 0.119 Angle : 0.614 9.359 28156 Z= 0.292 Chirality : 0.041 0.242 3010 Planarity : 0.004 0.044 3599 Dihedral : 7.557 59.907 3322 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.95 % Allowed : 27.51 % Favored : 67.53 % 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: 0.72 (0.18), residues: 2396 helix: 1.68 (0.13), residues: 1493 sheet: -3.88 (0.77), residues: 24 loop : -1.57 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 453 TYR 0.025 0.001 TYR 1 76 PHE 0.013 0.001 PHE 1 20 TRP 0.030 0.001 TRP 1 40 HIS 0.012 0.001 HIS A1124 Details of bonding type rmsd covalent geometry : bond 0.00264 (20589) covalent geometry : angle 0.59081 (28038) SS BOND : bond 0.00358 ( 11) SS BOND : angle 1.51829 ( 22) hydrogen bonds : bond 0.03695 ( 1068) hydrogen bonds : angle 4.02698 ( 3111) link_BETA1-4 : bond 0.00784 ( 16) link_BETA1-4 : angle 3.08061 ( 48) link_BETA1-6 : bond 0.00102 ( 1) link_BETA1-6 : angle 1.76519 ( 3) link_NAG-ASN : bond 0.00571 ( 15) link_NAG-ASN : angle 2.69155 ( 45) *********************** 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 284 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 181 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7859 (mt0) cc_final: 0.7600 (mp10) REVERT: A 60 LEU cc_start: 0.7587 (pp) cc_final: 0.6995 (tm) REVERT: A 62 GLN cc_start: 0.8124 (tp40) cc_final: 0.7777 (tm-30) REVERT: A 63 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 66 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 68 TRP cc_start: 0.7553 (m100) cc_final: 0.7115 (m100) REVERT: A 88 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6996 (tt) REVERT: A 108 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5959 (ttt90) REVERT: A 146 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 203 ASN cc_start: 0.7933 (t0) cc_final: 0.7331 (p0) REVERT: A 293 MET cc_start: 0.5033 (mpp) cc_final: 0.4606 (ptt) REVERT: A 306 LEU cc_start: 0.3888 (OUTLIER) cc_final: 0.3293 (mp) REVERT: A 352 THR cc_start: 0.4162 (OUTLIER) cc_final: 0.3066 (m) REVERT: A 353 MET cc_start: 0.6158 (tpt) cc_final: 0.5675 (pmt) REVERT: A 355 GLN cc_start: 0.5775 (tm-30) cc_final: 0.4960 (mp10) REVERT: A 393 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7436 (t0) REVERT: A 431 GLU cc_start: 0.8402 (tt0) cc_final: 0.8126 (tt0) REVERT: A 707 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7164 (mt-10) REVERT: A 763 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6171 (m-30) REVERT: A 859 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7705 (p90) REVERT: A 862 ILE cc_start: 0.3711 (OUTLIER) cc_final: 0.2914 (tp) REVERT: A 897 ASP cc_start: 0.8069 (t0) cc_final: 0.7697 (m-30) REVERT: A 989 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6821 (mt) REVERT: A 997 VAL cc_start: 0.6240 (p) cc_final: 0.5988 (m) REVERT: A 1119 HIS cc_start: 0.4488 (OUTLIER) cc_final: 0.2990 (t-90) REVERT: A 1124 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6575 (p90) REVERT: A 1143 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8057 (mtmt) REVERT: 1 283 MET cc_start: 0.5318 (mtt) cc_final: 0.4551 (mpt) REVERT: 1 293 MET cc_start: 0.6166 (pmm) cc_final: 0.5595 (pmm) REVERT: 1 348 CYS cc_start: 0.3057 (m) cc_final: 0.1878 (p) REVERT: 1 374 ASP cc_start: 0.7812 (m-30) cc_final: 0.6785 (t70) REVERT: 1 391 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7835 (mp) REVERT: 1 592 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.6061 (tp) REVERT: 1 677 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.5772 (pttm) REVERT: 1 743 ASN cc_start: 0.8152 (t0) cc_final: 0.7802 (t0) REVERT: 1 744 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7922 (p) REVERT: 1 875 MET cc_start: 0.2408 (mmt) cc_final: 0.2186 (mmt) REVERT: 1 987 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7151 (mm-30) outliers start: 103 outliers final: 74 residues processed: 264 average time/residue: 0.4137 time to fit residues: 130.1083 Evaluate side-chains 266 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 175 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 105 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 411 LEU Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 680 VAL Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 890 ARG Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 935 PHE Chi-restraints excluded: chain 1 residue 986 HIS Chi-restraints excluded: chain 1 residue 987 GLU Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1053 THR Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1102 SER Chi-restraints excluded: chain 1 residue 1105 ILE Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 88 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 213 optimal weight: 0.3980 chunk 177 optimal weight: 0.3980 chunk 142 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 189 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 950 ASN A1124 HIS A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** 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 = 0.4162 r_free = 0.4162 target = 0.174443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116156 restraints weight = 26467.555| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.41 r_work: 0.3337 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20632 Z= 0.114 Angle : 0.611 9.350 28156 Z= 0.291 Chirality : 0.040 0.244 3010 Planarity : 0.004 0.044 3599 Dihedral : 7.495 59.917 3322 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.52 % Allowed : 28.09 % Favored : 67.39 % 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: 0.76 (0.18), residues: 2396 helix: 1.71 (0.13), residues: 1492 sheet: -3.92 (0.77), residues: 24 loop : -1.56 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 453 TYR 0.039 0.001 TYR A 111 PHE 0.013 0.001 PHE 1 64 TRP 0.034 0.001 TRP 1 40 HIS 0.017 0.001 HIS A1124 Details of bonding type rmsd covalent geometry : bond 0.00246 (20589) covalent geometry : angle 0.58760 (28038) SS BOND : bond 0.00338 ( 11) SS BOND : angle 1.44345 ( 22) hydrogen bonds : bond 0.03588 ( 1068) hydrogen bonds : angle 3.99321 ( 3111) link_BETA1-4 : bond 0.00784 ( 16) link_BETA1-4 : angle 3.03775 ( 48) link_BETA1-6 : bond 0.00037 ( 1) link_BETA1-6 : angle 1.76560 ( 3) link_NAG-ASN : bond 0.00635 ( 15) link_NAG-ASN : angle 2.66768 ( 45) ********************** 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 278 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 184 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7901 (mt0) cc_final: 0.7638 (mp10) REVERT: A 60 LEU cc_start: 0.7552 (pp) cc_final: 0.6978 (tm) REVERT: A 62 GLN cc_start: 0.8113 (tp40) cc_final: 0.7721 (tm-30) REVERT: A 63 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 68 TRP cc_start: 0.7551 (m100) cc_final: 0.7137 (m100) REVERT: A 88 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7015 (tt) REVERT: A 108 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6039 (ttt90) REVERT: A 203 ASN cc_start: 0.8017 (t0) cc_final: 0.7439 (p0) REVERT: A 293 MET cc_start: 0.4959 (mpp) cc_final: 0.4491 (ptt) REVERT: A 306 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3256 (mp) REVERT: A 353 MET cc_start: 0.6179 (tpt) cc_final: 0.5721 (pmt) REVERT: A 393 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7590 (t0) REVERT: A 431 GLU cc_start: 0.8528 (tt0) cc_final: 0.8257 (tt0) REVERT: A 707 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7253 (mt-10) REVERT: A 763 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: A 859 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7851 (p90) REVERT: A 862 ILE cc_start: 0.3595 (OUTLIER) cc_final: 0.2712 (tp) REVERT: A 897 ASP cc_start: 0.8082 (t0) cc_final: 0.7698 (m-30) REVERT: A 916 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5582 (tmm) REVERT: A 989 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6875 (mt) REVERT: A 997 VAL cc_start: 0.6173 (p) cc_final: 0.5913 (m) REVERT: A 1143 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8028 (mtmt) REVERT: 1 278 ASP cc_start: 0.4350 (OUTLIER) cc_final: 0.3768 (m-30) REVERT: 1 283 MET cc_start: 0.5303 (mtt) cc_final: 0.4544 (mpt) REVERT: 1 293 MET cc_start: 0.6147 (pmm) cc_final: 0.5582 (pmm) REVERT: 1 348 CYS cc_start: 0.3202 (m) cc_final: 0.1930 (p) REVERT: 1 374 ASP cc_start: 0.7771 (m-30) cc_final: 0.6759 (t70) REVERT: 1 381 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7599 (mpp-170) REVERT: 1 391 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7874 (mp) REVERT: 1 592 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6154 (tp) REVERT: 1 677 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.5787 (pttm) REVERT: 1 709 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7314 (mm-30) REVERT: 1 743 ASN cc_start: 0.8199 (t0) cc_final: 0.7823 (t0) REVERT: 1 744 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7927 (p) REVERT: 1 875 MET cc_start: 0.2490 (mmt) cc_final: 0.2241 (mmt) outliers start: 94 outliers final: 71 residues processed: 261 average time/residue: 0.4421 time to fit residues: 136.9392 Evaluate side-chains 261 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 176 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain 1 residue 33 PHE Chi-restraints excluded: chain 1 residue 47 THR Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 105 LEU Chi-restraints excluded: chain 1 residue 127 VAL Chi-restraints excluded: chain 1 residue 242 ILE Chi-restraints excluded: chain 1 residue 269 VAL Chi-restraints excluded: chain 1 residue 278 ASP Chi-restraints excluded: chain 1 residue 279 VAL Chi-restraints excluded: chain 1 residue 304 LEU Chi-restraints excluded: chain 1 residue 319 LEU Chi-restraints excluded: chain 1 residue 352 THR Chi-restraints excluded: chain 1 residue 388 HIS Chi-restraints excluded: chain 1 residue 391 ILE Chi-restraints excluded: chain 1 residue 526 HIS Chi-restraints excluded: chain 1 residue 543 VAL Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 592 LEU Chi-restraints excluded: chain 1 residue 594 TRP Chi-restraints excluded: chain 1 residue 650 THR Chi-restraints excluded: chain 1 residue 677 LYS Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 816 LEU Chi-restraints excluded: chain 1 residue 846 ILE Chi-restraints excluded: chain 1 residue 890 ARG Chi-restraints excluded: chain 1 residue 902 LEU Chi-restraints excluded: chain 1 residue 915 SER Chi-restraints excluded: chain 1 residue 926 VAL Chi-restraints excluded: chain 1 residue 935 PHE Chi-restraints excluded: chain 1 residue 1023 LEU Chi-restraints excluded: chain 1 residue 1041 ASP Chi-restraints excluded: chain 1 residue 1078 THR Chi-restraints excluded: chain 1 residue 1098 ARG Chi-restraints excluded: chain 1 residue 1102 SER Chi-restraints excluded: chain 1 residue 1105 ILE Chi-restraints excluded: chain 1 residue 1186 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 141 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 231 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1124 HIS A1186 HIS ** 1 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11058 ASN ** 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 = 0.4144 r_free = 0.4144 target = 0.172663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117384 restraints weight = 26608.347| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.91 r_work: 0.3284 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20632 Z= 0.149 Angle : 0.637 9.383 28156 Z= 0.304 Chirality : 0.042 0.242 3010 Planarity : 0.004 0.044 3599 Dihedral : 7.584 59.985 3320 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.00 % Allowed : 27.90 % Favored : 67.10 % 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: 0.69 (0.18), residues: 2396 helix: 1.67 (0.14), residues: 1492 sheet: -3.94 (0.77), residues: 24 loop : -1.61 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 453 TYR 0.045 0.002 TYR 1 76 PHE 0.030 0.001 PHE A 64 TRP 0.032 0.001 TRP 1 40 HIS 0.006 0.001 HIS A1124 Details of bonding type rmsd covalent geometry : bond 0.00349 (20589) covalent geometry : angle 0.61418 (28038) SS BOND : bond 0.00364 ( 11) SS BOND : angle 1.50363 ( 22) hydrogen bonds : bond 0.03900 ( 1068) hydrogen bonds : angle 4.02875 ( 3111) link_BETA1-4 : bond 0.00763 ( 16) link_BETA1-4 : angle 3.03709 ( 48) link_BETA1-6 : bond 0.00083 ( 1) link_BETA1-6 : angle 1.69478 ( 3) link_NAG-ASN : bond 0.00555 ( 15) link_NAG-ASN : angle 2.74130 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7867.79 seconds wall clock time: 134 minutes 49.57 seconds (8089.57 seconds total)