Starting phenix.real_space_refine on Sun Jun 29 16:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqt_39505/06_2025/8yqt_39505_neut.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.122 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 189 5.16 5 C 22083 2.51 5 N 5921 2.21 5 O 6429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 1.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34629 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11227 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1344} Chain breaks: 2 Chain: "E" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 787 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "B" Number of atoms: 9530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1204, 9530 Classifications: {'peptide': 1204} Link IDs: {'PTRANS': 53, 'TRANS': 1150} Chain breaks: 4 Chain: "C" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2914 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2727 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain: "J" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4324 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 501} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 106.699 75.122 68.691 1.00 65.06 S ATOM 471 SG CYS A 62 104.464 73.911 65.872 1.00 60.79 S ATOM 531 SG CYS A 69 103.470 76.950 67.903 1.00 50.02 S ATOM 21064 SG CYS B1180 96.433 60.184 69.488 1.00 47.07 S ATOM 21089 SG CYS B1183 96.175 61.239 73.102 1.00 59.91 S ATOM 21205 SG CYS B1198 99.133 62.225 71.368 1.00 63.60 S ATOM 21227 SG CYS B1201 98.748 58.451 71.896 1.00 77.65 S ATOM 26177 SG CYS H 7 70.205 134.066 47.656 1.00 23.45 S ATOM 26201 SG CYS H 10 68.927 134.305 43.973 1.00 35.98 S ATOM 26620 SG CYS H 65 66.555 133.951 46.984 1.00 23.92 S ATOM 26626 SG CYS H 66 68.560 137.162 45.980 1.00 31.41 S ATOM 27323 SG CYS G 73 36.431 133.169 110.746 1.00 62.59 S ATOM 27344 SG CYS G 76 38.075 136.598 111.070 1.00 59.53 S ATOM 27501 SG CYS G 96 40.073 133.726 109.860 1.00 54.07 S ATOM 27518 SG CYS G 98 39.042 133.783 113.498 1.00 53.97 S ATOM 32341 SG CYS J 937 21.505 95.391 104.189 1.00 72.88 S ATOM 32443 SG CYS J 950 19.130 93.143 101.494 1.00101.47 S ATOM 32025 SG CYS J 898 20.755 115.220 75.722 1.00 68.77 S ATOM 32044 SG CYS J 901 18.338 117.688 76.944 1.00 62.09 S Time building chain proxies: 18.75, per 1000 atoms: 0.54 Number of scatterers: 34629 At special positions: 0 Unit cell: (147.864, 171.296, 176.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 189 16.00 Mg 1 11.99 O 6429 8.00 N 5921 7.00 C 22083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 7.58 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 62 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 59 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 69 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 98 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb=" ZN J1301 " pdb="ZN ZN J1301 " - pdb=" ND1 HIS J 943 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 937 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 950 " pdb=" ZN J1302 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 901 " pdb="ZN ZN J1302 " - pdb=" ND1 HIS J 857 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 898 " Number of angles added : 21 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 45 sheets defined 43.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.528A pdb=" N GLU A 113 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.707A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.980A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.533A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 448 through 451 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.532A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.699A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.635A pdb=" N MET A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.918A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.512A pdb=" N LEU A 657 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.830A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.662A pdb=" N PHE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.145A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 removed outlier: 3.654A pdb=" N LYS A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.950A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.525A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.513A pdb=" N ALA A 994 " --> pdb=" O TYR A 990 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1051 through 1059 removed outlier: 4.269A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.533A pdb=" N GLN A1078 " --> pdb=" O ILE A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1100 through 1106 removed outlier: 3.689A pdb=" N ASN A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.938A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 3.528A pdb=" N ARG A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1230 through 1235' Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.600A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.739A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.827A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 removed outlier: 3.975A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.833A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.546A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.757A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.830A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.874A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.743A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 355 through 372 removed outlier: 3.503A pdb=" N LYS B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.885A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.786A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 removed outlier: 3.585A pdb=" N SER B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 477 " --> pdb=" O ASN B 473 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.528A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.532A pdb=" N GLU B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 removed outlier: 3.634A pdb=" N LYS B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.575A pdb=" N LYS B 703 " --> pdb=" O ASP B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.675A pdb=" N GLU B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 804 removed outlier: 3.502A pdb=" N VAL B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.878A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 removed outlier: 3.598A pdb=" N LEU B1075 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.560A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.666A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.634A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.734A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.643A pdb=" N VAL D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.548A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.536A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.802A pdb=" N MET G 49 " --> pdb=" O THR G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 193 removed outlier: 4.039A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 removed outlier: 4.287A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 249 removed outlier: 3.528A pdb=" N LYS F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 314 removed outlier: 3.599A pdb=" N MET F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.671A pdb=" N ARG F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'J' and resid 673 through 683 removed outlier: 3.857A pdb=" N LEU J 683 " --> pdb=" O THR J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 697 removed outlier: 3.656A pdb=" N ASP J 697 " --> pdb=" O VAL J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 720 Processing helix chain 'J' and resid 722 through 728 Processing helix chain 'J' and resid 744 through 748 Processing helix chain 'J' and resid 774 through 790 Processing helix chain 'J' and resid 794 through 817 Processing helix chain 'J' and resid 845 through 849 Processing helix chain 'J' and resid 879 through 881 No H-bonds generated for 'chain 'J' and resid 879 through 881' Processing helix chain 'J' and resid 882 through 887 Processing helix chain 'J' and resid 907 through 911 removed outlier: 3.544A pdb=" N GLN J 910 " --> pdb=" O GLU J 907 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 933 Processing helix chain 'J' and resid 956 through 960 removed outlier: 3.686A pdb=" N ILE J 960 " --> pdb=" O THR J 957 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 977 removed outlier: 3.773A pdb=" N TYR J 973 " --> pdb=" O LEU J 969 " (cutoff:3.500A) Processing helix chain 'J' and resid 978 through 989 removed outlier: 3.659A pdb=" N ARG J 989 " --> pdb=" O LYS J 985 " (cutoff:3.500A) Processing helix chain 'J' and resid 1017 through 1028 Processing helix chain 'J' and resid 1030 through 1036 removed outlier: 4.023A pdb=" N ILE J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1044 through 1051 Processing helix chain 'J' and resid 1063 through 1085 removed outlier: 4.006A pdb=" N MET J1067 " --> pdb=" O ASP J1063 " (cutoff:3.500A) Processing helix chain 'J' and resid 1093 through 1098 removed outlier: 4.092A pdb=" N ARG J1098 " --> pdb=" O ILE J1094 " (cutoff:3.500A) Processing helix chain 'J' and resid 1104 through 1109 Processing helix chain 'J' and resid 1121 through 1133 Processing helix chain 'J' and resid 1133 through 1154 removed outlier: 3.606A pdb=" N LEU J1139 " --> pdb=" O ALA J1135 " (cutoff:3.500A) Processing helix chain 'J' and resid 1158 through 1182 removed outlier: 3.660A pdb=" N VAL J1162 " --> pdb=" O PRO J1158 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN J1163 " --> pdb=" O SER J1159 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE J1164 " --> pdb=" O TRP J1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU J1167 " --> pdb=" O ASN J1163 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE J1168 " --> pdb=" O ILE J1164 " (cutoff:3.500A) Processing helix chain 'J' and resid 1209 through 1213 Processing helix chain 'J' and resid 1242 through 1247 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.157A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.357A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.596A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 6.117A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.846A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.649A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.513A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1271 through 1278 removed outlier: 6.228A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 5.647A pdb=" N TRP A1174 " --> pdb=" O LEU A1227 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.780A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 161 removed outlier: 6.343A pdb=" N GLN B 145 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 140 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 147 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B 138 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG B 149 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER B 151 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 134 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA B 132 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 128 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 159 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLY B 126 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 removed outlier: 3.504A pdb=" N LEU B 204 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 217 removed outlier: 6.886A pdb=" N TYR B 250 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG B 229 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 248 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 231 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 246 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 233 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER B 244 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.557A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.688A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 7.079A pdb=" N LEU B 981 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 968 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 4.530A pdb=" N LYS B 995 " --> pdb=" O LEU B1111 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 894 through 896 Processing sheet with id=AD4, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD5, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.882A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS C 216 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N HIS C 186 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 67 through 73 removed outlier: 5.057A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AD9, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE1, first strand: chain 'D' and resid 20 through 21 removed outlier: 5.270A pdb=" N ILE D 52 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 87 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 117 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 138 through 142 removed outlier: 4.610A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AE4, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AE5, first strand: chain 'F' and resid 3 through 13 removed outlier: 6.635A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 3 through 13 Processing sheet with id=AE7, first strand: chain 'F' and resid 148 through 150 removed outlier: 4.893A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN F 95 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 237 through 238 removed outlier: 3.562A pdb=" N ALA F 270 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 875 through 878 removed outlier: 6.272A pdb=" N LYS J 865 " --> pdb=" O LEU J 893 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU J 893 " --> pdb=" O LYS J 865 " (cutoff:3.500A) 1523 hydrogen bonds defined for protein. 4170 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: 20.05 Time building geometry restraints manager: 9.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5737 1.30 - 1.43: 8814 1.43 - 1.56: 20468 1.56 - 1.69: 2 1.69 - 1.82: 308 Bond restraints: 35329 Sorted by residual: bond pdb=" C ILE A1074 " pdb=" O ILE A1074 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.19e-02 7.06e+03 3.25e+01 bond pdb=" CA TYR J 733 " pdb=" C TYR J 733 " ideal model delta sigma weight residual 1.522 1.451 0.070 1.31e-02 5.83e+03 2.87e+01 bond pdb=" CA GLN J 729 " pdb=" C GLN J 729 " ideal model delta sigma weight residual 1.525 1.476 0.049 1.11e-02 8.12e+03 1.99e+01 bond pdb=" C ASN B 860 " pdb=" O ASN B 860 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.32e-02 5.74e+03 1.92e+01 bond pdb=" CA ILE A1074 " pdb=" C ILE A1074 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.27e-02 6.20e+03 1.52e+01 ... (remaining 35324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 47437 2.57 - 5.14: 338 5.14 - 7.71: 37 7.71 - 10.28: 5 10.28 - 12.85: 4 Bond angle restraints: 47821 Sorted by residual: angle pdb=" N GLN J 747 " pdb=" CA GLN J 747 " pdb=" C GLN J 747 " ideal model delta sigma weight residual 113.30 100.69 12.61 1.34e+00 5.57e-01 8.86e+01 angle pdb=" N LEU J 748 " pdb=" CA LEU J 748 " pdb=" C LEU J 748 " ideal model delta sigma weight residual 113.20 102.04 11.16 1.21e+00 6.83e-01 8.51e+01 angle pdb=" C ARG J 750 " pdb=" CA ARG J 750 " pdb=" CB ARG J 750 " ideal model delta sigma weight residual 110.42 121.73 -11.31 1.99e+00 2.53e-01 3.23e+01 angle pdb=" N VAL A1075 " pdb=" CA VAL A1075 " pdb=" C VAL A1075 " ideal model delta sigma weight residual 111.67 106.62 5.05 9.50e-01 1.11e+00 2.83e+01 angle pdb=" N THR J 738 " pdb=" CA THR J 738 " pdb=" C THR J 738 " ideal model delta sigma weight residual 108.26 100.01 8.25 1.66e+00 3.63e-01 2.47e+01 ... (remaining 47816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 19591 17.79 - 35.58: 1409 35.58 - 53.37: 400 53.37 - 71.16: 97 71.16 - 88.95: 25 Dihedral angle restraints: 21522 sinusoidal: 8821 harmonic: 12701 Sorted by residual: dihedral pdb=" CA SER A1060 " pdb=" C SER A1060 " pdb=" N HIS A1061 " pdb=" CA HIS A1061 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE D 128 " pdb=" C ILE D 128 " pdb=" N ASN D 129 " pdb=" CA ASN D 129 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 21519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4968 0.085 - 0.169: 428 0.169 - 0.254: 2 0.254 - 0.338: 0 0.338 - 0.423: 2 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA ARG J 750 " pdb=" N ARG J 750 " pdb=" C ARG J 750 " pdb=" CB ARG J 750 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA LEU J 751 " pdb=" N LEU J 751 " pdb=" C LEU J 751 " pdb=" CB LEU J 751 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR J 741 " pdb=" N TYR J 741 " pdb=" C TYR J 741 " pdb=" CB TYR J 741 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5397 not shown) Planarity restraints: 6151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 727 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LEU J 727 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU J 727 " 0.023 2.00e-02 2.50e+03 pdb=" N SER J 728 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 153 " -0.057 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO B 154 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 732 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C PHE J 732 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE J 732 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR J 733 " -0.013 2.00e-02 2.50e+03 ... (remaining 6148 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 223 2.56 - 3.15: 26837 3.15 - 3.73: 53945 3.73 - 4.32: 81102 4.32 - 4.90: 132354 Nonbonded interactions: 294461 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A2001 " model vdw 1.978 2.170 nonbonded pdb=" ND2 ASN B1182 " pdb=" O GLN B1204 " model vdw 2.116 3.120 nonbonded pdb=" O SER B 436 " pdb=" OG1 THR B 474 " model vdw 2.120 3.040 nonbonded pdb=" OD2 ASP B1059 " pdb=" OG1 THR B1061 " model vdw 2.150 3.040 nonbonded pdb=" OG SER B 123 " pdb=" OE2 GLU B 483 " model vdw 2.181 3.040 ... (remaining 294456 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 88.540 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.089 35351 Z= 0.208 Angle : 0.600 12.847 47842 Z= 0.337 Chirality : 0.046 0.423 5400 Planarity : 0.004 0.083 6151 Dihedral : 14.296 88.948 13314 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.30 % Allowed : 11.31 % Favored : 87.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4297 helix: -0.42 (0.12), residues: 1637 sheet: -0.09 (0.20), residues: 612 loop : -0.34 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 257 HIS 0.008 0.001 HIS C 216 PHE 0.025 0.002 PHE A 918 TYR 0.018 0.001 TYR A1030 ARG 0.007 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.20174 ( 1511) hydrogen bonds : angle 7.36701 ( 4170) metal coordination : bond 0.00630 ( 22) metal coordination : angle 4.41374 ( 21) covalent geometry : bond 0.00428 (35329) covalent geometry : angle 0.59298 (47821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 448 time to evaluate : 6.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8884 (mmp) cc_final: 0.8676 (mmp) REVERT: J 731 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.4588 (mt-10) REVERT: J 813 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6605 (mtpt) outliers start: 50 outliers final: 28 residues processed: 488 average time/residue: 2.3090 time to fit residues: 1354.4918 Evaluate side-chains 452 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 422 time to evaluate : 10.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1182 ASN Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 731 GLU Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 813 LYS Chi-restraints excluded: chain J residue 1242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 101 ASN A 168 GLN A 264 GLN A 535 GLN A 642 ASN A 814 ASN A 834 GLN A 853 GLN A1018 GLN A1062 HIS A1090 GLN A1142 ASN A1296 ASN A1393 GLN A1405 ASN A1439 ASN B 43 ASN B 95 ASN B 207 ASN B 245 GLN B 261 ASN B 302 ASN B 328 ASN B 434 ASN B 484 GLN B 570 GLN B 598 GLN B1023 GLN C 19 ASN G 89 GLN F 121 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN J 729 GLN J1081 ASN J1102 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121454 restraints weight = 38002.148| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.74 r_work: 0.3304 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 35351 Z= 0.188 Angle : 0.586 15.190 47842 Z= 0.311 Chirality : 0.046 0.200 5400 Planarity : 0.005 0.054 6151 Dihedral : 5.683 57.569 4756 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.90 % Allowed : 9.62 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4297 helix: 0.47 (0.12), residues: 1664 sheet: -0.16 (0.20), residues: 605 loop : -0.28 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 466 HIS 0.007 0.001 HIS D 193 PHE 0.029 0.002 PHE A 918 TYR 0.017 0.002 TYR J1122 ARG 0.005 0.001 ARG J 721 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 1511) hydrogen bonds : angle 5.37260 ( 4170) metal coordination : bond 0.00586 ( 22) metal coordination : angle 4.14369 ( 21) covalent geometry : bond 0.00445 (35329) covalent geometry : angle 0.58004 (47821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 460 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6820 (mtt-85) REVERT: A 184 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7215 (mptt) REVERT: A 668 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: A 685 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 1027 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7305 (ttp80) REVERT: A 1093 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: E 66 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 196 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8132 (mmt90) REVERT: B 484 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8200 (mm-40) REVERT: B 601 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: B 806 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: B 905 LYS cc_start: 0.7247 (tmtp) cc_final: 0.6602 (mttm) REVERT: B 953 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7066 (mtt180) REVERT: C 9 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 28 LYS cc_start: 0.8023 (pptt) cc_final: 0.7822 (pptt) REVERT: C 277 THR cc_start: 0.8692 (m) cc_final: 0.8481 (t) REVERT: C 345 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: G 28 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: F 134 LEU cc_start: 0.6460 (mm) cc_final: 0.6228 (mm) REVERT: F 231 MET cc_start: -0.0079 (ttm) cc_final: -0.0724 (mpp) REVERT: J 721 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6043 (ptp90) REVERT: J 740 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.5913 (mptt) REVERT: J 747 GLN cc_start: 0.6646 (pt0) cc_final: 0.6236 (pt0) REVERT: J 1177 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7950 (mm) outliers start: 112 outliers final: 48 residues processed: 524 average time/residue: 1.5822 time to fit residues: 987.8130 Evaluate side-chains 490 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 427 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 721 ARG Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 740 LYS Chi-restraints excluded: chain J residue 746 THR Chi-restraints excluded: chain J residue 875 GLU Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1096 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 360 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 319 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 382 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A1296 ASN B 43 ASN B 207 ASN B 235 GLN B 302 ASN B 484 GLN B 516 ASN B 598 GLN B1142 HIS ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 729 GLN J1102 HIS J1117 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.168105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122812 restraints weight = 38118.535| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.73 r_work: 0.3309 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35351 Z= 0.159 Angle : 0.546 15.275 47842 Z= 0.288 Chirality : 0.045 0.188 5400 Planarity : 0.004 0.047 6151 Dihedral : 5.301 58.522 4737 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.96 % Allowed : 10.30 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4297 helix: 0.76 (0.13), residues: 1669 sheet: -0.15 (0.20), residues: 607 loop : -0.22 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1154 HIS 0.006 0.001 HIS D 193 PHE 0.027 0.002 PHE A 918 TYR 0.014 0.001 TYR A 574 ARG 0.006 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 1511) hydrogen bonds : angle 5.11988 ( 4170) metal coordination : bond 0.00538 ( 22) metal coordination : angle 4.02783 ( 21) covalent geometry : bond 0.00372 (35329) covalent geometry : angle 0.53913 (47821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 456 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7175 (ttp-110) REVERT: A 96 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.6971 (mtt-85) REVERT: A 236 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6974 (mtpt) REVERT: A 664 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7648 (mp-120) REVERT: A 668 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 685 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 1093 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 1124 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7698 (ptm160) REVERT: A 1253 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7167 (ptpt) REVERT: A 1359 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8576 (tp) REVERT: E 66 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 51 MET cc_start: 0.8865 (mmp) cc_final: 0.8648 (mmp) REVERT: B 203 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 601 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: B 806 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: B 905 LYS cc_start: 0.7336 (tmtp) cc_final: 0.6692 (mttm) REVERT: C 5 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6210 (p90) REVERT: C 9 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: C 52 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (ptt180) REVERT: C 285 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8311 (t0) REVERT: C 345 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: F 199 GLN cc_start: 0.3839 (mp10) cc_final: 0.3591 (mp10) REVERT: J 747 GLN cc_start: 0.7032 (pt0) cc_final: 0.6589 (pt0) REVERT: J 780 ARG cc_start: 0.7613 (tpt170) cc_final: 0.7345 (tpt170) REVERT: J 1047 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: J 1049 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6715 (ttm-80) REVERT: J 1160 TRP cc_start: 0.6260 (p-90) cc_final: 0.5975 (p-90) REVERT: J 1180 GLU cc_start: 0.7124 (tp30) cc_final: 0.6698 (tp30) outliers start: 114 outliers final: 47 residues processed: 529 average time/residue: 1.5688 time to fit residues: 989.6583 Evaluate side-chains 491 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 427 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 746 THR Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 1047 ASP Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 383 optimal weight: 8.9990 chunk 429 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 252 optimal weight: 0.1980 chunk 312 optimal weight: 0.2980 chunk 352 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 357 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 646 ASN A1296 ASN B 43 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B1142 HIS C 233 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 729 GLN J1079 ASN J1102 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.169286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124642 restraints weight = 38533.819| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.71 r_work: 0.3338 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35351 Z= 0.114 Angle : 0.505 15.781 47842 Z= 0.264 Chirality : 0.044 0.197 5400 Planarity : 0.004 0.042 6151 Dihedral : 4.910 57.665 4731 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.65 % Allowed : 11.31 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4297 helix: 1.02 (0.13), residues: 1666 sheet: -0.03 (0.20), residues: 620 loop : -0.12 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1154 HIS 0.006 0.001 HIS C 315 PHE 0.026 0.001 PHE A 918 TYR 0.013 0.001 TYR A1136 ARG 0.004 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1511) hydrogen bonds : angle 4.88999 ( 4170) metal coordination : bond 0.00441 ( 22) metal coordination : angle 3.63158 ( 21) covalent geometry : bond 0.00256 (35329) covalent geometry : angle 0.49958 (47821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 462 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7376 (ttm110) cc_final: 0.7065 (ttp-110) REVERT: A 96 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6781 (mtt-85) REVERT: A 123 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: A 236 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6859 (mtpt) REVERT: A 664 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7514 (mp-120) REVERT: A 668 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: A 685 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 1027 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: A 1093 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: A 1124 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7563 (ptm160) REVERT: A 1253 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7013 (ptpt) REVERT: A 1359 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8509 (tp) REVERT: E 66 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 51 MET cc_start: 0.8814 (mmp) cc_final: 0.8584 (mmp) REVERT: B 196 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8185 (mmt90) REVERT: B 203 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7665 (t0) REVERT: B 484 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8206 (mm-40) REVERT: B 584 LEU cc_start: 0.8459 (tt) cc_final: 0.8250 (tt) REVERT: B 588 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: B 601 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: B 888 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7791 (mm-30) REVERT: B 905 LYS cc_start: 0.7226 (tmtp) cc_final: 0.6574 (mttm) REVERT: B 953 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7159 (mtt-85) REVERT: C 1 MET cc_start: 0.3774 (tpt) cc_final: 0.3209 (tpp) REVERT: C 9 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: C 34 GLU cc_start: 0.7973 (mp0) cc_final: 0.7718 (pt0) REVERT: C 52 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8374 (ptt180) REVERT: C 211 THR cc_start: 0.9097 (m) cc_final: 0.8835 (p) REVERT: C 285 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8256 (t0) REVERT: C 345 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: D 83 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7221 (mtmt) REVERT: F 1 MET cc_start: 0.4637 (OUTLIER) cc_final: 0.3830 (mpt) REVERT: F 199 GLN cc_start: 0.3720 (mp10) cc_final: 0.3470 (mp10) REVERT: J 747 GLN cc_start: 0.7078 (pt0) cc_final: 0.6876 (pt0) REVERT: J 780 ARG cc_start: 0.7445 (tpt170) cc_final: 0.7149 (tpt170) REVERT: J 944 ASP cc_start: 0.7338 (t0) cc_final: 0.7087 (t0) REVERT: J 1049 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6677 (ttm-80) REVERT: J 1160 TRP cc_start: 0.6116 (p-90) cc_final: 0.5843 (p-90) REVERT: J 1180 GLU cc_start: 0.7043 (tp30) cc_final: 0.6583 (tp30) outliers start: 102 outliers final: 46 residues processed: 524 average time/residue: 1.5277 time to fit residues: 953.8795 Evaluate side-chains 505 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 440 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 36 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A1296 ASN B 43 ASN B 207 ASN B 302 ASN B 403 ASN B 484 GLN B 598 GLN B1142 HIS B1227 ASN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 729 GLN ** J1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122149 restraints weight = 38475.292| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.82 r_work: 0.3322 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35351 Z= 0.164 Angle : 0.542 15.634 47842 Z= 0.283 Chirality : 0.045 0.188 5400 Planarity : 0.004 0.045 6151 Dihedral : 4.917 53.841 4727 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.29 % Allowed : 11.18 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 4297 helix: 1.00 (0.13), residues: 1670 sheet: -0.04 (0.20), residues: 637 loop : -0.14 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1154 HIS 0.006 0.001 HIS D 193 PHE 0.027 0.002 PHE A 918 TYR 0.013 0.001 TYR A 574 ARG 0.006 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 1511) hydrogen bonds : angle 4.92472 ( 4170) metal coordination : bond 0.00504 ( 22) metal coordination : angle 3.92217 ( 21) covalent geometry : bond 0.00393 (35329) covalent geometry : angle 0.53561 (47821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 440 time to evaluate : 4.236 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7159 (ttp-110) REVERT: A 96 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6947 (mtt-85) REVERT: A 236 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6920 (mtpt) REVERT: A 517 MET cc_start: 0.8147 (mmm) cc_final: 0.7859 (ttp) REVERT: A 664 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7664 (mp-120) REVERT: A 668 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 685 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 1027 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7322 (ttp80) REVERT: A 1093 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: A 1253 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7231 (ptpt) REVERT: A 1359 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8535 (tp) REVERT: E 66 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 601 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: B 806 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: B 888 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7833 (mm-30) REVERT: C 1 MET cc_start: 0.3890 (tpt) cc_final: 0.3277 (tpp) REVERT: C 5 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6262 (p90) REVERT: C 9 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: C 34 GLU cc_start: 0.7981 (mp0) cc_final: 0.7747 (pt0) REVERT: C 52 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8397 (ptt180) REVERT: C 211 THR cc_start: 0.9092 (m) cc_final: 0.8859 (p) REVERT: C 256 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7535 (mt) REVERT: C 285 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8263 (t0) REVERT: C 345 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: D 148 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: F 1 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.3835 (mpt) REVERT: F 30 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: F 199 GLN cc_start: 0.3773 (mp10) cc_final: 0.3539 (mp10) REVERT: J 721 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.5712 (ptp90) REVERT: J 740 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6235 (mptt) REVERT: J 780 ARG cc_start: 0.7626 (tpt170) cc_final: 0.7356 (tpt170) REVERT: J 944 ASP cc_start: 0.7465 (t0) cc_final: 0.7199 (t0) REVERT: J 1047 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: J 1049 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6809 (ttm-80) REVERT: J 1050 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6639 (mp0) REVERT: J 1160 TRP cc_start: 0.6247 (p-90) cc_final: 0.6004 (p-90) REVERT: J 1180 GLU cc_start: 0.7112 (tp30) cc_final: 0.6636 (tp30) outliers start: 127 outliers final: 60 residues processed: 517 average time/residue: 1.6260 time to fit residues: 1003.7716 Evaluate side-chains 506 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 423 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 721 ARG Chi-restraints excluded: chain J residue 740 LYS Chi-restraints excluded: chain J residue 875 GLU Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 1047 ASP Chi-restraints excluded: chain J residue 1094 ILE Chi-restraints excluded: chain J residue 1096 VAL Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 160 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 121 optimal weight: 0.3980 chunk 306 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 413 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1018 GLN A1296 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B 972 HIS B1142 HIS C 233 GLN J 729 GLN ** J1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1102 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121313 restraints weight = 38377.720| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.80 r_work: 0.3310 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 35351 Z= 0.188 Angle : 0.566 15.160 47842 Z= 0.295 Chirality : 0.046 0.201 5400 Planarity : 0.004 0.051 6151 Dihedral : 4.988 55.403 4726 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.37 % Allowed : 11.28 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4297 helix: 0.93 (0.13), residues: 1669 sheet: -0.09 (0.20), residues: 633 loop : -0.16 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 257 HIS 0.008 0.001 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.015 0.002 TYR A 574 ARG 0.005 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 1511) hydrogen bonds : angle 4.96376 ( 4170) metal coordination : bond 0.00554 ( 22) metal coordination : angle 4.10226 ( 21) covalent geometry : bond 0.00454 (35329) covalent geometry : angle 0.55951 (47821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 434 time to evaluate : 3.908 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7157 (ttp-110) REVERT: A 96 ARG cc_start: 0.7376 (mtt-85) cc_final: 0.6801 (mtp180) REVERT: A 236 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6895 (mtpt) REVERT: A 517 MET cc_start: 0.8195 (mmm) cc_final: 0.7889 (ttp) REVERT: A 664 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7730 (mp-120) REVERT: A 668 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: A 685 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 1027 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7330 (ttp80) REVERT: A 1093 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: A 1124 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7341 (ptp-170) REVERT: A 1253 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7239 (ptpt) REVERT: A 1359 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (tp) REVERT: E 66 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (mp) REVERT: B 584 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8015 (tp) REVERT: B 601 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: B 888 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: C 1 MET cc_start: 0.3755 (tpt) cc_final: 0.3140 (tpp) REVERT: C 5 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6107 (p90) REVERT: C 9 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: C 52 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8399 (ptt180) REVERT: C 211 THR cc_start: 0.9103 (m) cc_final: 0.8869 (p) REVERT: C 256 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7544 (mt) REVERT: C 285 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8279 (t0) REVERT: C 345 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: D 83 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7196 (mtmt) REVERT: D 128 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7373 (pp) REVERT: F 1 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.3863 (mpt) REVERT: F 30 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: F 199 GLN cc_start: 0.3620 (mp10) cc_final: 0.3383 (mp10) REVERT: F 264 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4375 (mt) REVERT: J 780 ARG cc_start: 0.7632 (tpt170) cc_final: 0.7350 (tpt170) REVERT: J 944 ASP cc_start: 0.7463 (t0) cc_final: 0.7210 (t0) REVERT: J 1025 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7267 (ttpt) REVERT: J 1049 ARG cc_start: 0.6995 (ttm110) cc_final: 0.6752 (ttm-80) REVERT: J 1050 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6618 (mp0) REVERT: J 1160 TRP cc_start: 0.6222 (p-90) cc_final: 0.5976 (p-90) REVERT: J 1180 GLU cc_start: 0.7136 (tp30) cc_final: 0.6548 (tp30) outliers start: 130 outliers final: 60 residues processed: 514 average time/residue: 1.5853 time to fit residues: 969.0177 Evaluate side-chains 508 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 424 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1124 ARG Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 875 GLU Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 986 MET Chi-restraints excluded: chain J residue 1025 LYS Chi-restraints excluded: chain J residue 1047 ASP Chi-restraints excluded: chain J residue 1096 VAL Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 227 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A1296 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B1142 HIS C 233 GLN J 729 GLN J1102 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123664 restraints weight = 38468.654| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.73 r_work: 0.3327 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35351 Z= 0.132 Angle : 0.519 15.661 47842 Z= 0.270 Chirality : 0.044 0.193 5400 Planarity : 0.004 0.042 6151 Dihedral : 4.767 54.932 4725 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 12.01 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4297 helix: 1.06 (0.13), residues: 1670 sheet: -0.06 (0.20), residues: 630 loop : -0.10 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 257 HIS 0.006 0.001 HIS C 315 PHE 0.027 0.001 PHE F 306 TYR 0.012 0.001 TYR J1122 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1511) hydrogen bonds : angle 4.84146 ( 4170) metal coordination : bond 0.00479 ( 22) metal coordination : angle 3.76350 ( 21) covalent geometry : bond 0.00307 (35329) covalent geometry : angle 0.51334 (47821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 444 time to evaluate : 3.815 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7180 (ttp-110) REVERT: A 96 ARG cc_start: 0.7287 (mtt-85) cc_final: 0.6759 (mtp180) REVERT: A 236 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6907 (mtpt) REVERT: A 371 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7468 (mtm-85) REVERT: A 517 MET cc_start: 0.8141 (mmm) cc_final: 0.7891 (ttp) REVERT: A 664 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7749 (mp-120) REVERT: A 668 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: A 685 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 1027 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7326 (ttp80) REVERT: A 1179 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6854 (tt0) REVERT: A 1253 LYS cc_start: 0.7633 (pttp) cc_final: 0.7198 (ptpt) REVERT: B 51 MET cc_start: 0.8859 (mmp) cc_final: 0.8652 (mmp) REVERT: B 584 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 601 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: B 888 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: B 905 LYS cc_start: 0.7201 (tmtp) cc_final: 0.6843 (tmtp) REVERT: C 1 MET cc_start: 0.3744 (tpt) cc_final: 0.3132 (tpp) REVERT: C 5 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6169 (p90) REVERT: C 9 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: C 34 GLU cc_start: 0.7963 (mp0) cc_final: 0.7738 (pt0) REVERT: C 52 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (ptt180) REVERT: C 211 THR cc_start: 0.9071 (m) cc_final: 0.8840 (p) REVERT: C 345 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 83 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7233 (mtmt) REVERT: D 128 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7326 (pp) REVERT: F 1 MET cc_start: 0.4588 (OUTLIER) cc_final: 0.3688 (mpt) REVERT: F 199 GLN cc_start: 0.3700 (mp10) cc_final: 0.3491 (mp10) REVERT: F 216 GLU cc_start: 0.3884 (OUTLIER) cc_final: 0.2868 (tp30) REVERT: F 264 LEU cc_start: 0.4653 (OUTLIER) cc_final: 0.4370 (mt) REVERT: J 780 ARG cc_start: 0.7575 (tpt170) cc_final: 0.7297 (tpt170) REVERT: J 944 ASP cc_start: 0.7494 (t0) cc_final: 0.7241 (t0) REVERT: J 1025 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7289 (ttpt) REVERT: J 1049 ARG cc_start: 0.7032 (ttm110) cc_final: 0.6795 (ttm-80) REVERT: J 1050 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6610 (mp0) REVERT: J 1160 TRP cc_start: 0.6226 (p-90) cc_final: 0.5980 (p-90) REVERT: J 1180 GLU cc_start: 0.7009 (tp30) cc_final: 0.6478 (tp30) outliers start: 104 outliers final: 51 residues processed: 508 average time/residue: 1.5640 time to fit residues: 948.4946 Evaluate side-chains 501 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 432 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 1025 LYS Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 72 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 339 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A1296 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B 906 ASN B1142 HIS C 233 GLN J 729 GLN J1102 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122878 restraints weight = 38206.222| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.62 r_work: 0.3314 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35351 Z= 0.162 Angle : 0.547 15.544 47842 Z= 0.284 Chirality : 0.045 0.248 5400 Planarity : 0.004 0.044 6151 Dihedral : 4.824 55.307 4725 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.62 % Allowed : 12.34 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4297 helix: 1.03 (0.13), residues: 1670 sheet: -0.09 (0.20), residues: 639 loop : -0.12 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1154 HIS 0.007 0.001 HIS D 193 PHE 0.028 0.002 PHE F 306 TYR 0.013 0.001 TYR B 635 ARG 0.005 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 1511) hydrogen bonds : angle 4.86780 ( 4170) metal coordination : bond 0.00484 ( 22) metal coordination : angle 3.99881 ( 21) covalent geometry : bond 0.00388 (35329) covalent geometry : angle 0.54061 (47821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 431 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7160 (ttp-110) REVERT: A 96 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6744 (mtp180) REVERT: A 236 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6885 (mtpt) REVERT: A 664 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7731 (mp-120) REVERT: A 668 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 685 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 1027 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7298 (ttp80) REVERT: A 1124 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7331 (ptp-170) REVERT: A 1176 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 1179 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: A 1253 LYS cc_start: 0.7657 (pttp) cc_final: 0.7211 (ptpt) REVERT: B 64 ASN cc_start: 0.7391 (m-40) cc_final: 0.7011 (m-40) REVERT: B 196 ARG cc_start: 0.8364 (mmt90) cc_final: 0.8097 (mmt90) REVERT: B 484 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8211 (mm-40) REVERT: B 584 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8017 (tp) REVERT: B 601 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: B 888 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: C 5 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6115 (p90) REVERT: C 9 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: C 34 GLU cc_start: 0.7962 (mp0) cc_final: 0.7741 (pt0) REVERT: C 52 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (ptt180) REVERT: C 211 THR cc_start: 0.9107 (m) cc_final: 0.8869 (p) REVERT: C 256 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7582 (mt) REVERT: C 345 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: D 83 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7243 (mtmt) REVERT: D 128 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7322 (pp) REVERT: F 1 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.3769 (mpt) REVERT: F 140 TYR cc_start: 0.7090 (m-10) cc_final: 0.6808 (m-10) REVERT: F 199 GLN cc_start: 0.3530 (mp10) cc_final: 0.3297 (mp10) REVERT: F 216 GLU cc_start: 0.3898 (OUTLIER) cc_final: 0.3041 (tp30) REVERT: F 264 LEU cc_start: 0.4626 (OUTLIER) cc_final: 0.4328 (mt) REVERT: J 780 ARG cc_start: 0.7555 (tpt170) cc_final: 0.7270 (tpt170) REVERT: J 936 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.5433 (mpt180) REVERT: J 944 ASP cc_start: 0.7495 (t0) cc_final: 0.7235 (t0) REVERT: J 1047 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: J 1049 ARG cc_start: 0.7009 (ttm110) cc_final: 0.6733 (ttm-80) REVERT: J 1160 TRP cc_start: 0.6205 (p-90) cc_final: 0.5962 (p-90) outliers start: 101 outliers final: 57 residues processed: 492 average time/residue: 1.5671 time to fit residues: 918.7591 Evaluate side-chains 503 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 423 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1124 ARG Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 936 ARG Chi-restraints excluded: chain J residue 986 MET Chi-restraints excluded: chain J residue 1047 ASP Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 364 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 355 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 382 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 349 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A1296 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B 906 ASN B 972 HIS B1142 HIS C 233 GLN J 729 GLN J1102 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122023 restraints weight = 38452.717| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.78 r_work: 0.3313 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35351 Z= 0.163 Angle : 0.550 15.572 47842 Z= 0.285 Chirality : 0.045 0.270 5400 Planarity : 0.004 0.044 6151 Dihedral : 4.825 55.459 4725 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.62 % Allowed : 12.50 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4297 helix: 1.02 (0.13), residues: 1670 sheet: -0.08 (0.20), residues: 639 loop : -0.12 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1154 HIS 0.007 0.001 HIS D 193 PHE 0.027 0.002 PHE A 918 TYR 0.013 0.001 TYR B 635 ARG 0.008 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 1511) hydrogen bonds : angle 4.86865 ( 4170) metal coordination : bond 0.00487 ( 22) metal coordination : angle 3.96831 ( 21) covalent geometry : bond 0.00389 (35329) covalent geometry : angle 0.54386 (47821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 424 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7121 (ttp-110) REVERT: A 96 ARG cc_start: 0.7237 (mtt-85) cc_final: 0.6685 (mtp180) REVERT: A 236 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6812 (mtpt) REVERT: A 664 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7684 (mp-120) REVERT: A 668 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: A 685 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 1027 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7263 (ttp80) REVERT: A 1124 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7301 (ptp-170) REVERT: A 1176 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 1179 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: A 1253 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7126 (ptpt) REVERT: B 196 ARG cc_start: 0.8366 (mmt90) cc_final: 0.8129 (mmt90) REVERT: B 484 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8186 (mm-40) REVERT: B 584 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7963 (tp) REVERT: B 601 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: B 888 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: C 5 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6039 (p90) REVERT: C 9 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 34 GLU cc_start: 0.7927 (mp0) cc_final: 0.7684 (pt0) REVERT: C 52 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (ptt180) REVERT: C 211 THR cc_start: 0.9081 (m) cc_final: 0.8834 (p) REVERT: C 256 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7533 (mt) REVERT: C 345 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: D 83 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7164 (mtmt) REVERT: D 128 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7282 (pp) REVERT: F 1 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.3718 (mpt) REVERT: F 199 GLN cc_start: 0.3470 (mp10) cc_final: 0.3263 (mp10) REVERT: F 216 GLU cc_start: 0.3930 (OUTLIER) cc_final: 0.3086 (tp30) REVERT: F 264 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4375 (mt) REVERT: J 780 ARG cc_start: 0.7487 (tpt170) cc_final: 0.7202 (tpt170) REVERT: J 936 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.5417 (mpt180) REVERT: J 944 ASP cc_start: 0.7461 (t0) cc_final: 0.7191 (t0) REVERT: J 1047 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: J 1049 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6609 (ttp-170) REVERT: J 1160 TRP cc_start: 0.6126 (p-90) cc_final: 0.5878 (p-90) outliers start: 101 outliers final: 60 residues processed: 485 average time/residue: 1.5873 time to fit residues: 923.8718 Evaluate side-chains 507 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 423 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1124 ARG Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain J residue 682 LEU Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 936 ARG Chi-restraints excluded: chain J residue 986 MET Chi-restraints excluded: chain J residue 1047 ASP Chi-restraints excluded: chain J residue 1170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 232 optimal weight: 0.7980 chunk 217 optimal weight: 0.2980 chunk 345 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 342 optimal weight: 0.8980 chunk 407 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1296 ASN B 207 ASN B 302 ASN B 484 GLN B 598 GLN B 906 ASN B1142 HIS C 233 GLN J1102 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126965 restraints weight = 37672.928| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.67 r_work: 0.3348 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35351 Z= 0.106 Angle : 0.504 16.091 47842 Z= 0.261 Chirality : 0.043 0.272 5400 Planarity : 0.004 0.041 6151 Dihedral : 4.596 54.407 4725 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.00 % Allowed : 13.10 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4297 helix: 1.17 (0.13), residues: 1674 sheet: -0.05 (0.20), residues: 623 loop : -0.05 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1154 HIS 0.005 0.001 HIS C 315 PHE 0.027 0.001 PHE F 197 TYR 0.011 0.001 TYR J1122 ARG 0.004 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 1511) hydrogen bonds : angle 4.75119 ( 4170) metal coordination : bond 0.00416 ( 22) metal coordination : angle 3.63390 ( 21) covalent geometry : bond 0.00236 (35329) covalent geometry : angle 0.49839 (47821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 449 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7176 (ttp-110) REVERT: A 96 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6701 (mtp180) REVERT: A 123 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: A 236 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6852 (mtpt) REVERT: A 425 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8482 (ptt180) REVERT: A 517 MET cc_start: 0.8103 (mmm) cc_final: 0.7894 (ttp) REVERT: A 664 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7698 (mp-120) REVERT: A 668 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 685 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 1027 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7348 (ttp80) REVERT: A 1176 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7877 (tp) REVERT: B 51 MET cc_start: 0.8855 (mmp) cc_final: 0.8643 (mmp) REVERT: B 97 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 484 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (mm110) REVERT: B 584 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7960 (tp) REVERT: B 601 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: B 888 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7805 (mm-30) REVERT: B 1139 LYS cc_start: 0.7080 (mttm) cc_final: 0.5922 (ttmm) REVERT: C 5 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6132 (p90) REVERT: C 34 GLU cc_start: 0.7972 (mp0) cc_final: 0.7751 (pt0) REVERT: C 211 THR cc_start: 0.9073 (m) cc_final: 0.8844 (p) REVERT: C 345 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: D 83 LYS cc_start: 0.7423 (mtpt) cc_final: 0.7114 (mtmt) REVERT: D 128 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7225 (pp) REVERT: H 32 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7467 (mmmt) REVERT: F 1 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.3604 (mpt) REVERT: F 264 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4317 (mt) REVERT: J 780 ARG cc_start: 0.7520 (tpt170) cc_final: 0.7223 (tpt170) REVERT: J 936 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.5408 (mpt180) REVERT: J 944 ASP cc_start: 0.7450 (t0) cc_final: 0.7203 (t0) REVERT: J 1049 ARG cc_start: 0.7029 (ttm110) cc_final: 0.6676 (ttp-170) REVERT: J 1160 TRP cc_start: 0.6142 (p-90) cc_final: 0.5895 (p-90) outliers start: 77 outliers final: 44 residues processed: 495 average time/residue: 1.6741 time to fit residues: 997.7584 Evaluate side-chains 494 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 433 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1191 SER Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1179 ILE Chi-restraints excluded: chain B residue 1197 LYS Chi-restraints excluded: chain B residue 1199 MET Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 908 VAL Chi-restraints excluded: chain J residue 936 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 188 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 51 optimal weight: 0.0000 chunk 276 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 379 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A1296 ASN B 207 ASN B 302 ASN B 598 GLN B 906 ASN B1142 HIS J1102 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.170294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126128 restraints weight = 38085.384| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.64 r_work: 0.3335 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35351 Z= 0.109 Angle : 0.507 15.948 47842 Z= 0.262 Chirality : 0.044 0.271 5400 Planarity : 0.004 0.041 6151 Dihedral : 4.513 53.362 4723 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.82 % Allowed : 13.59 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4297 helix: 1.21 (0.13), residues: 1678 sheet: -0.03 (0.20), residues: 616 loop : -0.02 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1154 HIS 0.005 0.001 HIS C 315 PHE 0.025 0.001 PHE A 918 TYR 0.011 0.001 TYR B 635 ARG 0.006 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 1511) hydrogen bonds : angle 4.69710 ( 4170) metal coordination : bond 0.00394 ( 22) metal coordination : angle 3.55497 ( 21) covalent geometry : bond 0.00248 (35329) covalent geometry : angle 0.50195 (47821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35018.52 seconds wall clock time: 600 minutes 43.87 seconds (36043.87 seconds total)