Starting phenix.real_space_refine on Mon Sep 14 18:40:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hlr_0240/09_2026/6hlr_0240.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 163 5.16 5 C 20227 2.51 5 N 5638 2.21 5 O 6259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32370 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11513 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 8 Chain: "B" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9254 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 59, 'TRANS': 1104} Chain breaks: 3 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1740 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 486 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 732 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 67.801 53.021 56.297 1.00 50.78 S ATOM 480 SG CYS A 65 71.538 51.208 55.864 1.00 50.84 S ATOM 535 SG CYS A 72 70.705 53.247 59.089 1.00 48.46 S ATOM 781 SG CYS A 102 69.856 103.080 45.403 1.00 67.10 S ATOM 806 SG CYS A 105 72.362 102.233 42.704 1.00 67.02 S ATOM 1597 SG CYS A 233 73.571 104.560 45.185 1.00 73.09 S ATOM 1619 SG CYS A 236 70.930 105.579 41.657 1.00 76.35 S ATOM 20097 SG CYS B1104 82.614 61.529 48.510 1.00 46.57 S ATOM 20123 SG CYS B1107 80.436 64.412 48.262 1.00 47.49 S ATOM 20270 SG CYS B1128 79.033 61.182 48.775 1.00 51.02 S ATOM 28713 SG CYS I 10 41.777 128.141 102.488 1.00 72.65 S ATOM 28735 SG CYS I 13 40.843 124.444 101.572 1.00 71.80 S ATOM 28855 SG CYS I 30 41.647 126.408 98.505 1.00 82.07 S ATOM 29190 SG CYS J 7 87.266 42.622 126.948 1.00 36.77 S ATOM 29213 SG CYS J 10 90.633 41.675 127.804 1.00 37.82 S ATOM 29493 SG CYS J 45 90.497 45.869 128.200 1.00 35.42 S ATOM 29499 SG CYS J 46 88.547 43.189 130.297 1.00 35.94 S ATOM 30514 SG CYS L 31 46.342 41.803 110.103 1.00 55.21 S ATOM 30534 SG CYS L 34 44.557 40.432 112.982 1.00 58.44 S ATOM 30638 SG CYS L 48 43.556 38.862 109.822 1.00 69.94 S ATOM 30661 SG CYS L 51 42.636 43.100 111.308 1.00 68.64 S Time building chain proxies: 6.07, per 1000 atoms: 0.19 Number of scatterers: 32370 At special positions: 0 Unit cell: (166.4, 162.24, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 163 16.00 P 76 15.00 Mg 1 11.99 O 6259 8.00 N 5638 7.00 C 20227 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 21 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7288 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 51 sheets defined 37.4% alpha, 18.5% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.507A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.726A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.663A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.568A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.812A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 228 removed outlier: 3.733A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.797A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.855A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.832A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 439 removed outlier: 3.971A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.515A pdb=" N ALA A 459 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.811A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.853A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.601A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.569A pdb=" N THR A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.533A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.878A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 658 " --> pdb=" O SER A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.617A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.016A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.552A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.506A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 4.042A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.660A pdb=" N ASP A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 851 removed outlier: 3.698A pdb=" N VAL A 851 " --> pdb=" O LYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.534A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.579A pdb=" N VAL A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.780A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1011 Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.913A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.531A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.550A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.025A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 3.637A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 4.136A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.599A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.878A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.811A pdb=" N PHE A1166 " --> pdb=" O ASN A1162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.984A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1248 through 1253 removed outlier: 3.623A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.643A pdb=" N ILE A1258 " --> pdb=" O PHE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.604A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.517A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.824A pdb=" N LEU A1324 " --> pdb=" O GLN A1320 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.538A pdb=" N ARG A1444 " --> pdb=" O ASN A1440 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.166A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A1516 " --> pdb=" O GLU A1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1516' Processing helix chain 'A' and resid 1527 through 1531 removed outlier: 3.628A pdb=" N TRP A1530 " --> pdb=" O GLN A1527 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A1531 " --> pdb=" O ALA A1528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1527 through 1531' Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.967A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1554 removed outlier: 3.513A pdb=" N GLY A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1568 removed outlier: 3.583A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.777A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.620A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 4.075A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.666A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.144A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.205A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 69 removed outlier: 4.007A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.663A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.624A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.687A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.592A pdb=" N ALA B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.650A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.547A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.077A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.668A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.746A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 407 through 434 removed outlier: 3.556A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.818A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.661A pdb=" N ALA B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 506 through 511' Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.775A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.629A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.718A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.560A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.592A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.556A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.749A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 838' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.642A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.993A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.550A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.542A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 Processing helix chain 'B' and resid 1180 through 1193 removed outlier: 3.533A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.527A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.563A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 removed outlier: 4.072A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.497A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.975A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 179' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.572A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 277 through 286 removed outlier: 5.319A pdb=" N GLU C 283 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU C 284 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.564A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 Processing helix chain 'D' and resid 44 through 49 removed outlier: 3.506A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.551A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.792A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.981A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.790A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.543A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.716A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 4.033A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.646A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.917A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 67 removed outlier: 4.126A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 51 removed outlier: 4.097A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.712A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 131 Processing helix chain 'K' and resid 132 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 removed outlier: 3.583A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 486 removed outlier: 3.875A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.072A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.799A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.458A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.666A pdb=" N MET B 787 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TRP B 931 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 789 " --> pdb=" O TRP B 931 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 948 through 949 removed outlier: 3.746A pdb=" N GLY A 948 " --> pdb=" O VAL A 982 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id=AB5, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.700A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1459 through 1462 removed outlier: 4.354A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU I 45 " --> pdb=" O THR A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.887A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.724A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 96 through 104 removed outlier: 3.657A pdb=" N SER B 144 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 143 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 96 through 104 removed outlier: 3.657A pdb=" N SER B 144 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.274A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.893A pdb=" N TYR B 252 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR B 232 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU B 250 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 234 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 248 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 236 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN B 246 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.580A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC8, first strand: chain 'B' and resid 571 through 572 removed outlier: 7.068A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.550A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.550A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD3, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.817A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD5, first strand: chain 'B' and resid 1010 through 1011 Processing sheet with id=AD6, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD7, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id=AD9, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.696A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.368A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.195A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE4, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.796A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE6, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.234A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.234A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.752A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.702A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 245 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS G 158 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF5, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 1138 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9859 1.33 - 1.46: 6374 1.46 - 1.58: 16507 1.58 - 1.70: 147 1.70 - 1.82: 260 Bond restraints: 33147 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.611 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.609 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C4 G2P T3000 " pdb=" C5 G2P T3000 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C3' DC T 37 " pdb=" C2' DC T 37 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 ... (remaining 33142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 43622 2.36 - 4.71: 1305 4.71 - 7.07: 140 7.07 - 9.42: 49 9.42 - 11.78: 5 Bond angle restraints: 45121 Sorted by residual: angle pdb=" N ILE B 696 " pdb=" CA ILE B 696 " pdb=" C ILE B 696 " ideal model delta sigma weight residual 112.96 105.96 7.00 1.00e+00 1.00e+00 4.91e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 122.46 129.49 -7.03 1.41e+00 5.03e-01 2.48e+01 angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" O4' DC T 18 " pdb=" C4' DC T 18 " pdb=" C3' DC T 18 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 ... (remaining 45116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 18675 17.47 - 34.93: 918 34.93 - 52.40: 292 52.40 - 69.86: 80 69.86 - 87.33: 14 Dihedral angle restraints: 19979 sinusoidal: 8695 harmonic: 11284 Sorted by residual: dihedral pdb=" CA GLN I 41 " pdb=" C GLN I 41 " pdb=" N PHE I 42 " pdb=" CA PHE I 42 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LYS A 463 " pdb=" C LYS A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 19976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3892 0.066 - 0.132: 967 0.132 - 0.198: 158 0.198 - 0.265: 27 0.265 - 0.331: 4 Chirality restraints: 5048 Sorted by residual: chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 5045 not shown) Planarity restraints: 5572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " 0.030 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR B1033 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO E 151 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B1044 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C PHE B1044 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B1044 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN B1045 " 0.018 2.00e-02 2.50e+03 ... (remaining 5569 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 28 2.37 - 3.00: 15109 3.00 - 3.63: 47372 3.63 - 4.27: 77021 4.27 - 4.90: 126122 Nonbonded interactions: 265652 Sorted by model distance: nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1701 " model vdw 1.734 2.170 nonbonded pdb=" O3' C R 20 " pdb="MG MG A1701 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG A1701 " model vdw 2.144 2.170 nonbonded pdb=" OD2 ASP B 843 " pdb=" OH TYR L 29 " model vdw 2.213 3.040 nonbonded pdb=" O PHE B 963 " pdb=" OH TYR B1027 " model vdw 2.228 3.040 ... (remaining 265647 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.730 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.009 0.527 33169 Z= 0.377 Angle : 1.007 35.435 45142 Z= 0.537 Chirality : 0.060 0.331 5048 Planarity : 0.007 0.083 5572 Dihedral : 12.470 87.329 12691 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.10), residues: 3827 helix: -4.31 (0.06), residues: 1248 sheet: -2.30 (0.19), residues: 547 loop : -2.05 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 920 TYR 0.053 0.003 TYR B1033 PHE 0.038 0.003 PHE A 637 TRP 0.049 0.004 TRP B 836 HIS 0.016 0.002 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.33 (33147) covalent geometry : angle 0.95698 / 0.53 (45121) hydrogen bonds : bond 0.29946 / 19.65 ( 1155) hydrogen bonds : angle 10.53019 / 7.34 ( 3232) metal coordination : bond 0.20226 / 13.01 ( 22) metal coordination : angle 14.61349 / 10.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 980 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8707 (t) cc_final: 0.8363 (t) REVERT: A 416 ARG cc_start: 0.6716 (ttt180) cc_final: 0.6377 (ttm110) REVERT: A 1078 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8342 (mmmt) REVERT: A 1170 MET cc_start: 0.8876 (mmp) cc_final: 0.8593 (mmt) REVERT: A 1579 PHE cc_start: 0.8014 (m-80) cc_final: 0.7719 (m-80) REVERT: A 1587 ASP cc_start: 0.8454 (m-30) cc_final: 0.7958 (m-30) REVERT: A 1648 ASN cc_start: 0.8017 (m-40) cc_final: 0.7640 (t0) REVERT: B 108 MET cc_start: 0.8345 (mmt) cc_final: 0.7318 (mmt) REVERT: B 388 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 427 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7663 (tp40) REVERT: B 698 SER cc_start: 0.9006 (p) cc_final: 0.8694 (t) REVERT: B 707 SER cc_start: 0.9267 (t) cc_final: 0.8996 (m) REVERT: B 778 TYR cc_start: 0.8908 (t80) cc_final: 0.7942 (t80) REVERT: B 824 HIS cc_start: 0.8101 (m-70) cc_final: 0.7314 (m-70) REVERT: B 834 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8630 (mmtm) REVERT: B 1061 LYS cc_start: 0.8457 (tttm) cc_final: 0.7960 (tttt) REVERT: B 1065 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7104 (mtp180) REVERT: C 34 GLU cc_start: 0.7917 (mp0) cc_final: 0.7651 (mp0) REVERT: C 128 ASP cc_start: 0.8211 (p0) cc_final: 0.7527 (p0) REVERT: C 226 SER cc_start: 0.8706 (p) cc_final: 0.8384 (m) REVERT: C 319 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7791 (mtt-85) REVERT: D 34 ASP cc_start: 0.7833 (m-30) cc_final: 0.7518 (t70) REVERT: E 8 ASN cc_start: 0.8037 (m-40) cc_final: 0.7543 (m-40) REVERT: E 187 TYR cc_start: 0.8939 (t80) cc_final: 0.8572 (t80) REVERT: F 123 LYS cc_start: 0.8641 (tttt) cc_final: 0.8015 (ttpt) REVERT: G 52 MET cc_start: 0.8271 (ptm) cc_final: 0.8025 (ptm) REVERT: G 236 VAL cc_start: 0.8149 (t) cc_final: 0.7914 (m) REVERT: H 27 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7018 (mt-10) REVERT: H 100 THR cc_start: 0.8801 (m) cc_final: 0.8514 (p) REVERT: H 145 ARG cc_start: 0.8447 (ttm170) cc_final: 0.7956 (ttp-170) REVERT: J 31 ASP cc_start: 0.8317 (p0) cc_final: 0.8072 (p0) REVERT: K 85 ASP cc_start: 0.7853 (t0) cc_final: 0.7392 (t0) REVERT: K 112 THR cc_start: 0.9179 (p) cc_final: 0.8560 (p) REVERT: K 119 LYS cc_start: 0.8360 (tttt) cc_final: 0.8025 (tmtt) REVERT: K 126 ASP cc_start: 0.7765 (m-30) cc_final: 0.7263 (m-30) outliers start: 5 outliers final: 3 residues processed: 984 average time/residue: 0.2321 time to fit residues: 354.8894 Evaluate side-chains 578 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 575 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 260 GLN A 470 HIS A 489 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A1062 HIS A1199 GLN A1250 GLN A1453 HIS A1527 GLN A1633 GLN A1647 ASN A1648 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 480 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 710 ASN B 718 GLN B 745 GLN B 921 HIS B 952 HIS B1045 GLN B1199 ASN C 172 GLN C 175 GLN C 207 HIS ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 78 GLN G 65 HIS ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN H 35 GLN K 106 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105017 restraints weight = 47212.442| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.79 r_work: 0.3099 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 33169 Z= 0.150 Angle : 0.678 11.927 45142 Z= 0.359 Chirality : 0.046 0.213 5048 Planarity : 0.006 0.058 5572 Dihedral : 13.188 85.862 5035 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.21 % Allowed : 10.63 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.12), residues: 3827 helix: -2.19 (0.12), residues: 1261 sheet: -1.75 (0.20), residues: 563 loop : -1.50 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 146 TYR 0.020 0.002 TYR B 655 PHE 0.026 0.002 PHE A 108 TRP 0.023 0.001 TRP B 836 HIS 0.015 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (33147) covalent geometry : angle 0.67279 / 0.36 (45121) hydrogen bonds : bond 0.05812 / 3.71 ( 1155) hydrogen bonds : angle 6.02494 / 4.16 ( 3232) metal coordination : bond 0.02068 / 1.43 ( 22) metal coordination : angle 3.95398 / 2.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 621 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: A 187 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 188 TYR cc_start: 0.9021 (t80) cc_final: 0.8817 (t80) REVERT: A 416 ARG cc_start: 0.6927 (ttt180) cc_final: 0.6375 (ttm110) REVERT: A 516 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 570 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 604 LYS cc_start: 0.8678 (mttt) cc_final: 0.8342 (mtpt) REVERT: A 1004 GLU cc_start: 0.8652 (tp30) cc_final: 0.8451 (tp30) REVERT: A 1175 MET cc_start: 0.9471 (ttm) cc_final: 0.9060 (ttm) REVERT: A 1234 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7825 (mttt) REVERT: A 1332 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8355 (mm-30) REVERT: A 1459 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7760 (mtmt) REVERT: B 351 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8107 (tp-100) REVERT: B 397 THR cc_start: 0.9371 (t) cc_final: 0.9047 (m) REVERT: B 557 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7691 (t0) REVERT: B 785 ASP cc_start: 0.8475 (m-30) cc_final: 0.8189 (m-30) REVERT: B 1061 LYS cc_start: 0.8660 (tttm) cc_final: 0.8008 (tttt) REVERT: B 1065 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7787 (mtp180) REVERT: C 34 GLU cc_start: 0.8526 (mp0) cc_final: 0.8138 (mp0) REVERT: C 39 ASP cc_start: 0.8810 (m-30) cc_final: 0.8605 (m-30) REVERT: C 128 ASP cc_start: 0.8250 (p0) cc_final: 0.7998 (p0) REVERT: C 174 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7961 (ptp90) REVERT: C 226 SER cc_start: 0.8929 (p) cc_final: 0.8617 (m) REVERT: C 319 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8347 (mtt-85) REVERT: D 34 ASP cc_start: 0.8409 (m-30) cc_final: 0.7805 (t70) REVERT: D 35 GLU cc_start: 0.7984 (mp0) cc_final: 0.7656 (mp0) REVERT: E 45 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8027 (ttpp) REVERT: E 187 TYR cc_start: 0.9186 (t80) cc_final: 0.8717 (t80) REVERT: G 40 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7568 (ttp80) REVERT: G 52 MET cc_start: 0.8670 (ptm) cc_final: 0.8245 (ptm) REVERT: G 64 GLN cc_start: 0.8932 (mt0) cc_final: 0.8669 (mt0) REVERT: G 148 LEU cc_start: 0.6276 (mt) cc_final: 0.6068 (mp) REVERT: H 27 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7765 (mt-10) REVERT: H 100 THR cc_start: 0.9052 (m) cc_final: 0.8670 (p) REVERT: H 129 TYR cc_start: 0.8539 (p90) cc_final: 0.8242 (p90) REVERT: H 136 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8305 (mttp) REVERT: K 67 GLU cc_start: 0.8448 (pt0) cc_final: 0.8149 (pt0) REVERT: K 85 ASP cc_start: 0.8428 (t0) cc_final: 0.7898 (t0) REVERT: K 119 LYS cc_start: 0.8597 (tttt) cc_final: 0.8235 (tmtt) REVERT: K 122 LYS cc_start: 0.8675 (tptt) cc_final: 0.8215 (tptt) REVERT: K 126 ASP cc_start: 0.8356 (m-30) cc_final: 0.8062 (m-30) REVERT: K 141 SER cc_start: 0.8552 (t) cc_final: 0.8263 (p) REVERT: L 33 GLU cc_start: 0.9073 (tp30) cc_final: 0.8752 (mm-30) outliers start: 76 outliers final: 37 residues processed: 671 average time/residue: 0.2094 time to fit residues: 224.6408 Evaluate side-chains 570 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 528 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 1234 LYS Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 9 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 304 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 191 optimal weight: 0.3980 chunk 218 optimal weight: 7.9990 chunk 382 optimal weight: 50.0000 chunk 52 optimal weight: 0.2980 chunk 145 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN A1250 GLN A1447 GLN A1453 HIS B 499 HIS B1165 ASN B1199 ASN C 161 HIS C 172 GLN C 216 HIS E 8 ASN E 99 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 78 GLN G 119 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106010 restraints weight = 47169.648| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.81 r_work: 0.3107 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33169 Z= 0.115 Angle : 0.586 11.124 45142 Z= 0.311 Chirality : 0.044 0.194 5048 Planarity : 0.004 0.045 5572 Dihedral : 13.001 84.427 5035 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.62 % Allowed : 12.23 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3827 helix: -0.93 (0.14), residues: 1245 sheet: -1.38 (0.20), residues: 590 loop : -1.16 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 634 TYR 0.018 0.001 TYR B 655 PHE 0.023 0.001 PHE B1167 TRP 0.017 0.001 TRP B 836 HIS 0.011 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (33147) covalent geometry : angle 0.58350 / 0.31 (45121) hydrogen bonds : bond 0.04372 / 2.79 ( 1155) hydrogen bonds : angle 5.37591 / 3.71 ( 3232) metal coordination : bond 0.00412 / 0.26 ( 22) metal coordination : angle 2.65857 / 1.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 583 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 244 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7919 (ttt90) REVERT: A 413 LEU cc_start: 0.3956 (OUTLIER) cc_final: 0.3681 (tt) REVERT: A 416 ARG cc_start: 0.7012 (ttt180) cc_final: 0.6478 (ttm110) REVERT: A 516 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 547 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 570 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8782 (p) REVERT: A 604 LYS cc_start: 0.8787 (mttt) cc_final: 0.8438 (mtpt) REVERT: A 846 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9224 (mp) REVERT: A 1004 GLU cc_start: 0.8651 (tp30) cc_final: 0.8337 (tp30) REVERT: A 1175 MET cc_start: 0.9374 (ttm) cc_final: 0.9057 (ttm) REVERT: A 1459 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7827 (mtmt) REVERT: B 190 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8912 (pp) REVERT: B 307 GLU cc_start: 0.8538 (tt0) cc_final: 0.8332 (tt0) REVERT: B 351 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8169 (tp-100) REVERT: B 785 ASP cc_start: 0.8516 (m-30) cc_final: 0.8219 (m-30) REVERT: B 1136 GLU cc_start: 0.7302 (pt0) cc_final: 0.6641 (tm-30) REVERT: C 128 ASP cc_start: 0.8219 (p0) cc_final: 0.7989 (p0) REVERT: C 174 ARG cc_start: 0.8298 (ptp90) cc_final: 0.7837 (ptp-170) REVERT: C 226 SER cc_start: 0.8900 (p) cc_final: 0.8580 (m) REVERT: C 319 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8373 (mtt-85) REVERT: C 327 TYR cc_start: 0.8481 (t80) cc_final: 0.8191 (t80) REVERT: D 34 ASP cc_start: 0.8489 (m-30) cc_final: 0.7849 (t70) REVERT: D 35 GLU cc_start: 0.7959 (mp0) cc_final: 0.7644 (mp0) REVERT: E 45 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8121 (ttpp) REVERT: E 187 TYR cc_start: 0.9199 (t80) cc_final: 0.8754 (t80) REVERT: G 40 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7357 (ttp-110) REVERT: G 148 LEU cc_start: 0.6541 (mt) cc_final: 0.6312 (mp) REVERT: G 234 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6360 (ttp-170) REVERT: H 27 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7638 (mt-10) REVERT: H 100 THR cc_start: 0.8978 (m) cc_final: 0.8629 (p) REVERT: H 129 TYR cc_start: 0.8565 (p90) cc_final: 0.8336 (p90) REVERT: H 136 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8226 (mttp) REVERT: H 138 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: H 144 ILE cc_start: 0.9491 (mm) cc_final: 0.9254 (mt) REVERT: I 37 TYR cc_start: 0.8223 (m-80) cc_final: 0.8018 (m-80) REVERT: K 67 GLU cc_start: 0.8548 (pt0) cc_final: 0.8312 (pt0) REVERT: K 85 ASP cc_start: 0.8456 (t0) cc_final: 0.8045 (t0) REVERT: K 119 LYS cc_start: 0.8580 (tttt) cc_final: 0.8159 (tmtt) REVERT: K 122 LYS cc_start: 0.8647 (tptt) cc_final: 0.8063 (tptt) REVERT: K 126 ASP cc_start: 0.8444 (m-30) cc_final: 0.7936 (m-30) REVERT: L 33 GLU cc_start: 0.9115 (tp30) cc_final: 0.8852 (mm-30) REVERT: L 40 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8699 (mp) outliers start: 90 outliers final: 48 residues processed: 646 average time/residue: 0.2098 time to fit residues: 216.9527 Evaluate side-chains 577 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 521 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 137 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS A1088 HIS A1250 GLN A1293 HIS A1453 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 720 GLN B1165 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095823 restraints weight = 47106.676| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.80 r_work: 0.2955 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 33169 Z= 0.369 Angle : 0.768 11.202 45142 Z= 0.398 Chirality : 0.052 0.249 5048 Planarity : 0.005 0.058 5572 Dihedral : 13.047 82.137 5032 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.05 % Allowed : 12.14 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 3827 helix: -0.72 (0.14), residues: 1269 sheet: -1.28 (0.20), residues: 573 loop : -1.06 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 920 TYR 0.031 0.003 TYR B1033 PHE 0.029 0.003 PHE A 637 TRP 0.025 0.002 TRP B 836 HIS 0.013 0.002 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.37 (33147) covalent geometry : angle 0.76372 / 0.40 (45121) hydrogen bonds : bond 0.04880 / 3.15 ( 1155) hydrogen bonds : angle 5.34956 / 3.68 ( 3232) metal coordination : bond 0.01009 / 0.65 ( 22) metal coordination : angle 3.84290 / 2.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 495 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8424 (tmm) cc_final: 0.7728 (ttt) REVERT: A 413 LEU cc_start: 0.3775 (OUTLIER) cc_final: 0.3556 (tt) REVERT: A 416 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6640 (ttm110) REVERT: A 420 PHE cc_start: 0.8250 (t80) cc_final: 0.7770 (t80) REVERT: A 547 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9092 (mp) REVERT: A 604 LYS cc_start: 0.8703 (mttt) cc_final: 0.8437 (mtpt) REVERT: A 846 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9273 (mp) REVERT: A 1004 GLU cc_start: 0.8622 (tp30) cc_final: 0.8380 (tp30) REVERT: A 1175 MET cc_start: 0.9423 (ttm) cc_final: 0.9180 (ttm) REVERT: A 1459 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7860 (ttmt) REVERT: A 1555 VAL cc_start: 0.8985 (t) cc_final: 0.8775 (p) REVERT: B 190 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8957 (pp) REVERT: B 307 GLU cc_start: 0.8618 (tt0) cc_final: 0.8389 (tt0) REVERT: B 351 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8460 (tp-100) REVERT: B 685 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8633 (t) REVERT: B 785 ASP cc_start: 0.8716 (m-30) cc_final: 0.8368 (m-30) REVERT: B 944 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: B 1040 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8681 (p) REVERT: C 226 SER cc_start: 0.9151 (p) cc_final: 0.8845 (m) REVERT: C 319 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8340 (mtt-85) REVERT: C 327 TYR cc_start: 0.8478 (t80) cc_final: 0.8163 (t80) REVERT: D 35 GLU cc_start: 0.8166 (mp0) cc_final: 0.7790 (mp0) REVERT: E 45 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8162 (ttpp) REVERT: G 40 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7586 (ttp-110) REVERT: G 234 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6377 (ttp-170) REVERT: H 27 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7886 (mt-10) REVERT: H 45 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 100 THR cc_start: 0.9103 (m) cc_final: 0.8683 (p) REVERT: H 129 TYR cc_start: 0.8619 (p90) cc_final: 0.8239 (p90) REVERT: H 138 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: I 15 ASP cc_start: 0.8852 (t0) cc_final: 0.8560 (t70) REVERT: K 67 GLU cc_start: 0.8639 (pt0) cc_final: 0.8372 (pt0) REVERT: K 85 ASP cc_start: 0.8658 (t0) cc_final: 0.7945 (t0) REVERT: K 119 LYS cc_start: 0.8676 (tttt) cc_final: 0.8281 (tttm) REVERT: K 126 ASP cc_start: 0.8507 (m-30) cc_final: 0.8278 (m-30) REVERT: L 33 GLU cc_start: 0.9239 (tp30) cc_final: 0.9016 (mm-30) REVERT: L 40 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8824 (mp) outliers start: 139 outliers final: 89 residues processed: 590 average time/residue: 0.2046 time to fit residues: 196.2807 Evaluate side-chains 560 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 462 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 292 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 374 optimal weight: 0.7980 chunk 378 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS A1250 GLN A1453 HIS B 480 GLN B 767 ASN B1199 ASN C 172 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099989 restraints weight = 46519.961| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.80 r_work: 0.3017 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33169 Z= 0.144 Angle : 0.603 9.703 45142 Z= 0.315 Chirality : 0.045 0.161 5048 Planarity : 0.004 0.068 5572 Dihedral : 12.926 80.682 5032 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.00 % Allowed : 14.09 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 3827 helix: -0.13 (0.15), residues: 1257 sheet: -1.13 (0.20), residues: 579 loop : -0.78 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1444 TYR 0.021 0.002 TYR A1104 PHE 0.028 0.001 PHE B1167 TRP 0.021 0.001 TRP B 836 HIS 0.012 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (33147) covalent geometry : angle 0.59911 / 0.32 (45121) hydrogen bonds : bond 0.03811 / 2.45 ( 1155) hydrogen bonds : angle 5.01446 / 3.44 ( 3232) metal coordination : bond 0.00510 / 0.31 ( 22) metal coordination : angle 3.07162 / 2.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 528 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7981 (ttt90) REVERT: A 413 LEU cc_start: 0.3910 (OUTLIER) cc_final: 0.3678 (tt) REVERT: A 416 ARG cc_start: 0.6868 (ttt180) cc_final: 0.6555 (ttm110) REVERT: A 604 LYS cc_start: 0.8683 (mttt) cc_final: 0.8384 (mtpt) REVERT: A 846 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9283 (mp) REVERT: A 1004 GLU cc_start: 0.8564 (tp30) cc_final: 0.8354 (tp30) REVERT: A 1234 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7969 (mttt) REVERT: A 1459 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7703 (mtmt) REVERT: B 66 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7923 (ttmm) REVERT: B 190 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8883 (pp) REVERT: B 307 GLU cc_start: 0.8550 (tt0) cc_final: 0.8344 (tt0) REVERT: B 679 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7729 (mp10) REVERT: B 785 ASP cc_start: 0.8643 (m-30) cc_final: 0.8330 (m-30) REVERT: B 787 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: B 944 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: C 174 ARG cc_start: 0.8382 (ptp-170) cc_final: 0.8042 (ptp90) REVERT: C 226 SER cc_start: 0.9058 (p) cc_final: 0.8778 (m) REVERT: C 319 ARG cc_start: 0.8806 (tpp80) cc_final: 0.8351 (mtt-85) REVERT: C 327 TYR cc_start: 0.8409 (t80) cc_final: 0.8130 (t80) REVERT: D 35 GLU cc_start: 0.8116 (mp0) cc_final: 0.7791 (mp0) REVERT: E 45 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8168 (ttpp) REVERT: E 63 ASN cc_start: 0.8533 (m-40) cc_final: 0.8315 (m-40) REVERT: G 40 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7501 (ttp-110) REVERT: G 234 ARG cc_start: 0.6906 (ttt180) cc_final: 0.6497 (ttp-170) REVERT: H 27 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7804 (mt-10) REVERT: H 45 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7308 (tm-30) REVERT: H 100 THR cc_start: 0.8975 (m) cc_final: 0.8642 (p) REVERT: H 137 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: I 15 ASP cc_start: 0.8852 (t0) cc_final: 0.8584 (t70) REVERT: K 67 GLU cc_start: 0.8621 (pt0) cc_final: 0.8387 (pt0) REVERT: K 85 ASP cc_start: 0.8538 (t0) cc_final: 0.7891 (t0) REVERT: K 119 LYS cc_start: 0.8636 (tttt) cc_final: 0.8203 (tttm) REVERT: K 126 ASP cc_start: 0.8516 (m-30) cc_final: 0.8234 (m-30) REVERT: L 40 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8814 (mp) outliers start: 103 outliers final: 64 residues processed: 596 average time/residue: 0.2086 time to fit residues: 199.7805 Evaluate side-chains 556 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 483 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1234 LYS Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 214 optimal weight: 8.9990 chunk 364 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 chunk 201 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 349 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 171 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN A 603 HIS ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1250 GLN A1453 HIS B 975 HIS C 172 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098943 restraints weight = 46778.860| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.78 r_work: 0.3000 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33169 Z= 0.167 Angle : 0.595 9.780 45142 Z= 0.312 Chirality : 0.045 0.156 5048 Planarity : 0.004 0.051 5572 Dihedral : 12.882 81.184 5032 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.09 % Allowed : 14.56 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 3827 helix: 0.16 (0.15), residues: 1255 sheet: -1.01 (0.20), residues: 577 loop : -0.66 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 634 TYR 0.020 0.001 TYR A1302 PHE 0.020 0.001 PHE B 508 TRP 0.017 0.001 TRP B 836 HIS 0.010 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (33147) covalent geometry : angle 0.59223 / 0.31 (45121) hydrogen bonds : bond 0.03745 / 2.41 ( 1155) hydrogen bonds : angle 4.88974 / 3.35 ( 3232) metal coordination : bond 0.00500 / 0.32 ( 22) metal coordination : angle 2.80248 / 1.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 498 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8030 (ttt90) REVERT: A 416 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6524 (ttm110) REVERT: A 604 LYS cc_start: 0.8713 (mttt) cc_final: 0.8398 (mtpt) REVERT: A 846 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9254 (mp) REVERT: A 1459 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7750 (mtmt) REVERT: A 1471 GLU cc_start: 0.8318 (tp30) cc_final: 0.8020 (mm-30) REVERT: B 164 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8779 (ptp) REVERT: B 190 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8906 (pp) REVERT: B 679 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7748 (mp10) REVERT: B 783 MET cc_start: 0.8547 (mtt) cc_final: 0.8096 (mtt) REVERT: B 785 ASP cc_start: 0.8684 (m-30) cc_final: 0.8355 (m-30) REVERT: B 912 GLN cc_start: 0.8713 (mp10) cc_final: 0.8490 (mm110) REVERT: B 944 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8419 (mt0) REVERT: B 1040 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8595 (p) REVERT: C 174 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.7962 (ptp90) REVERT: C 226 SER cc_start: 0.9064 (p) cc_final: 0.8794 (m) REVERT: C 319 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8373 (mtt-85) REVERT: C 327 TYR cc_start: 0.8423 (t80) cc_final: 0.8143 (t80) REVERT: D 35 GLU cc_start: 0.8131 (mp0) cc_final: 0.7807 (mp0) REVERT: E 45 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8088 (ttpp) REVERT: E 63 ASN cc_start: 0.8530 (m-40) cc_final: 0.8308 (m-40) REVERT: G 40 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7606 (ttp-110) REVERT: G 234 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6514 (ttp-170) REVERT: H 27 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7890 (mt-10) REVERT: H 45 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7261 (tm-30) REVERT: H 100 THR cc_start: 0.8985 (m) cc_final: 0.8681 (p) REVERT: H 136 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8434 (mtmm) REVERT: K 67 GLU cc_start: 0.8608 (pt0) cc_final: 0.8342 (pt0) REVERT: K 85 ASP cc_start: 0.8552 (t0) cc_final: 0.8032 (t0) REVERT: K 119 LYS cc_start: 0.8628 (tttt) cc_final: 0.8220 (tttm) REVERT: K 126 ASP cc_start: 0.8538 (m-30) cc_final: 0.8278 (m-30) REVERT: L 40 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (mp) outliers start: 106 outliers final: 79 residues processed: 562 average time/residue: 0.2132 time to fit residues: 193.4904 Evaluate side-chains 561 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 476 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 123 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 370 optimal weight: 0.0670 chunk 295 optimal weight: 0.9990 chunk 386 optimal weight: 50.0000 chunk 207 optimal weight: 9.9990 chunk 384 optimal weight: 50.0000 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1250 GLN A1453 HIS B 896 GLN C 172 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 64 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097306 restraints weight = 46791.564| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.83 r_work: 0.2975 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33169 Z= 0.166 Angle : 0.591 9.523 45142 Z= 0.309 Chirality : 0.045 0.158 5048 Planarity : 0.004 0.052 5572 Dihedral : 12.855 81.188 5032 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 15.20 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3827 helix: 0.33 (0.15), residues: 1261 sheet: -0.99 (0.20), residues: 588 loop : -0.53 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 634 TYR 0.019 0.001 TYR A1104 PHE 0.019 0.001 PHE B 508 TRP 0.018 0.001 TRP B 836 HIS 0.010 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (33147) covalent geometry : angle 0.58775 / 0.31 (45121) hydrogen bonds : bond 0.03623 / 2.33 ( 1155) hydrogen bonds : angle 4.79851 / 3.29 ( 3232) metal coordination : bond 0.00509 / 0.32 ( 22) metal coordination : angle 2.71473 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 497 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8391 (tmm) cc_final: 0.7796 (ttp) REVERT: A 244 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8054 (ttt90) REVERT: A 416 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6535 (ttm110) REVERT: A 490 ILE cc_start: 0.8764 (mm) cc_final: 0.8501 (mt) REVERT: A 604 LYS cc_start: 0.8678 (mttt) cc_final: 0.8363 (mtpt) REVERT: A 846 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9183 (mt) REVERT: A 1234 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: A 1459 LYS cc_start: 0.8323 (tmtt) cc_final: 0.7752 (mtmt) REVERT: A 1471 GLU cc_start: 0.8221 (tp30) cc_final: 0.8006 (mm-30) REVERT: A 1555 VAL cc_start: 0.8975 (t) cc_final: 0.8762 (p) REVERT: B 66 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (ttmm) REVERT: B 164 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8791 (ptp) REVERT: B 190 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8923 (pp) REVERT: B 679 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7794 (mp10) REVERT: B 785 ASP cc_start: 0.8692 (m-30) cc_final: 0.8366 (m-30) REVERT: B 944 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: B 1037 ARG cc_start: 0.9193 (ptt90) cc_final: 0.8903 (ptm-80) REVERT: B 1040 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (p) REVERT: C 174 ARG cc_start: 0.8301 (ptp-170) cc_final: 0.7960 (ptp90) REVERT: C 226 SER cc_start: 0.9084 (p) cc_final: 0.8825 (m) REVERT: C 319 ARG cc_start: 0.8816 (tpp80) cc_final: 0.8340 (mtt-85) REVERT: C 327 TYR cc_start: 0.8463 (t80) cc_final: 0.8139 (t80) REVERT: D 35 GLU cc_start: 0.8152 (mp0) cc_final: 0.7736 (mp0) REVERT: E 45 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8080 (ttpp) REVERT: E 63 ASN cc_start: 0.8500 (m-40) cc_final: 0.8299 (m-40) REVERT: G 40 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7837 (ttp80) REVERT: G 234 ARG cc_start: 0.6955 (ttt180) cc_final: 0.6510 (ttp-170) REVERT: H 27 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7889 (mt-10) REVERT: H 45 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7314 (tm-30) REVERT: H 86 ASP cc_start: 0.7921 (m-30) cc_final: 0.7709 (m-30) REVERT: H 100 THR cc_start: 0.8974 (m) cc_final: 0.8688 (p) REVERT: H 133 ASN cc_start: 0.8476 (t0) cc_final: 0.8191 (m110) REVERT: H 136 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8650 (mtmt) REVERT: K 67 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: K 85 ASP cc_start: 0.8602 (t0) cc_final: 0.8119 (t0) REVERT: K 119 LYS cc_start: 0.8653 (tttt) cc_final: 0.8240 (tttm) REVERT: K 126 ASP cc_start: 0.8512 (m-30) cc_final: 0.8243 (m-30) REVERT: K 140 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8285 (mttm) REVERT: L 40 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8856 (mp) outliers start: 108 outliers final: 80 residues processed: 566 average time/residue: 0.2004 time to fit residues: 183.0937 Evaluate side-chains 567 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 478 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1234 LYS Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 254 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 384 optimal weight: 50.0000 chunk 130 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 380 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS A1509 HIS B 923 GLN B1094 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.095697 restraints weight = 46737.657| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.82 r_work: 0.2952 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 33169 Z= 0.231 Angle : 0.630 9.705 45142 Z= 0.328 Chirality : 0.047 0.274 5048 Planarity : 0.004 0.053 5572 Dihedral : 12.876 81.451 5032 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.23 % Allowed : 15.49 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3827 helix: 0.33 (0.15), residues: 1264 sheet: -0.99 (0.21), residues: 568 loop : -0.54 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 146 TYR 0.021 0.002 TYR A1302 PHE 0.018 0.002 PHE B 508 TRP 0.018 0.001 TRP B 836 HIS 0.010 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (33147) covalent geometry : angle 0.62726 / 0.33 (45121) hydrogen bonds : bond 0.03822 / 2.47 ( 1155) hydrogen bonds : angle 4.83342 / 3.31 ( 3232) metal coordination : bond 0.00658 / 0.41 ( 22) metal coordination : angle 2.93239 / 1.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 479 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8363 (tmm) cc_final: 0.7790 (ttp) REVERT: A 244 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8016 (ttt90) REVERT: A 333 CYS cc_start: 0.8854 (p) cc_final: 0.8646 (t) REVERT: A 416 ARG cc_start: 0.6915 (ttt180) cc_final: 0.6392 (ttm110) REVERT: A 490 ILE cc_start: 0.8833 (mm) cc_final: 0.8545 (mt) REVERT: A 604 LYS cc_start: 0.8692 (mttt) cc_final: 0.8379 (mtpt) REVERT: A 846 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9224 (mp) REVERT: A 1459 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7722 (mtmt) REVERT: A 1471 GLU cc_start: 0.8240 (tp30) cc_final: 0.8027 (mm-30) REVERT: A 1555 VAL cc_start: 0.9009 (t) cc_final: 0.8791 (p) REVERT: B 164 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8788 (ptp) REVERT: B 190 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 515 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 679 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7860 (mp10) REVERT: B 783 MET cc_start: 0.8567 (mtt) cc_final: 0.8141 (mtt) REVERT: B 785 ASP cc_start: 0.8747 (m-30) cc_final: 0.8429 (m-30) REVERT: B 944 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: B 1037 ARG cc_start: 0.9243 (ptt90) cc_final: 0.9036 (ptm-80) REVERT: B 1040 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8665 (p) REVERT: C 174 ARG cc_start: 0.8282 (ptp-170) cc_final: 0.7947 (ptp90) REVERT: C 226 SER cc_start: 0.9139 (p) cc_final: 0.8883 (m) REVERT: C 319 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8346 (mtt-85) REVERT: C 327 TYR cc_start: 0.8503 (t80) cc_final: 0.8187 (t80) REVERT: D 35 GLU cc_start: 0.8184 (mp0) cc_final: 0.7783 (mp0) REVERT: E 45 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8085 (ttpp) REVERT: G 234 ARG cc_start: 0.6969 (ttt180) cc_final: 0.6530 (ttp-170) REVERT: H 27 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7912 (mt-10) REVERT: H 45 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7475 (tm-30) REVERT: H 86 ASP cc_start: 0.7992 (m-30) cc_final: 0.7726 (m-30) REVERT: H 100 THR cc_start: 0.9008 (m) cc_final: 0.8756 (p) REVERT: H 133 ASN cc_start: 0.8515 (t0) cc_final: 0.8237 (m110) REVERT: H 136 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8688 (mtmt) REVERT: J 25 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9079 (mp) REVERT: K 67 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: K 85 ASP cc_start: 0.8612 (t0) cc_final: 0.8070 (t0) REVERT: K 119 LYS cc_start: 0.8629 (tttt) cc_final: 0.8250 (tttm) REVERT: K 126 ASP cc_start: 0.8541 (m-30) cc_final: 0.8283 (m-30) REVERT: K 140 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8289 (mttm) REVERT: L 40 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8861 (mp) outliers start: 111 outliers final: 87 residues processed: 549 average time/residue: 0.2004 time to fit residues: 176.8252 Evaluate side-chains 560 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 464 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 224 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 283 optimal weight: 0.3980 chunk 284 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN C 172 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN H 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097613 restraints weight = 46421.325| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.75 r_work: 0.2994 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33169 Z= 0.187 Angle : 0.608 9.328 45142 Z= 0.318 Chirality : 0.046 0.229 5048 Planarity : 0.004 0.057 5572 Dihedral : 12.865 81.097 5032 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 15.81 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 3827 helix: 0.42 (0.15), residues: 1265 sheet: -0.96 (0.21), residues: 566 loop : -0.49 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 634 TYR 0.019 0.002 TYR A1302 PHE 0.017 0.001 PHE B1167 TRP 0.018 0.001 TRP B 836 HIS 0.009 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (33147) covalent geometry : angle 0.60513 / 0.32 (45121) hydrogen bonds : bond 0.03663 / 2.36 ( 1155) hydrogen bonds : angle 4.79036 / 3.28 ( 3232) metal coordination : bond 0.00575 / 0.36 ( 22) metal coordination : angle 2.89467 / 1.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 486 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8433 (tmm) cc_final: 0.7436 (ttt) REVERT: A 63 SER cc_start: 0.8865 (m) cc_final: 0.8658 (p) REVERT: A 188 TYR cc_start: 0.9047 (t80) cc_final: 0.8835 (t80) REVERT: A 244 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7973 (ttt90) REVERT: A 416 ARG cc_start: 0.6867 (ttt180) cc_final: 0.6359 (ttm110) REVERT: A 490 ILE cc_start: 0.8804 (mm) cc_final: 0.8502 (mt) REVERT: A 604 LYS cc_start: 0.8657 (mttt) cc_final: 0.8391 (mtpt) REVERT: A 846 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9182 (mt) REVERT: A 1459 LYS cc_start: 0.8316 (tmtt) cc_final: 0.7711 (mtmt) REVERT: A 1471 GLU cc_start: 0.8231 (tp30) cc_final: 0.8023 (mm-30) REVERT: B 164 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8790 (ptp) REVERT: B 190 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8923 (pp) REVERT: B 515 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7990 (t) REVERT: B 679 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7823 (mp10) REVERT: B 785 ASP cc_start: 0.8753 (m-30) cc_final: 0.8436 (m-30) REVERT: B 944 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: B 1037 ARG cc_start: 0.9260 (ptt90) cc_final: 0.8988 (ptm-80) REVERT: C 174 ARG cc_start: 0.8174 (ptp-170) cc_final: 0.7874 (ptp90) REVERT: C 226 SER cc_start: 0.9047 (p) cc_final: 0.8827 (m) REVERT: C 319 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8380 (mtt-85) REVERT: C 327 TYR cc_start: 0.8464 (t80) cc_final: 0.8083 (t80) REVERT: D 35 GLU cc_start: 0.8196 (mp0) cc_final: 0.7721 (mp0) REVERT: E 45 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8096 (ttpp) REVERT: E 122 LYS cc_start: 0.7928 (mmtp) cc_final: 0.6805 (pttm) REVERT: G 234 ARG cc_start: 0.6958 (ttt180) cc_final: 0.6522 (ttp-170) REVERT: H 27 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7881 (mt-10) REVERT: H 45 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7463 (tm-30) REVERT: H 133 ASN cc_start: 0.8521 (t0) cc_final: 0.8251 (m110) REVERT: J 25 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9102 (mp) REVERT: K 67 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: K 85 ASP cc_start: 0.8567 (t0) cc_final: 0.8094 (t0) REVERT: K 119 LYS cc_start: 0.8642 (tttt) cc_final: 0.8292 (tmtt) REVERT: K 126 ASP cc_start: 0.8567 (m-30) cc_final: 0.8332 (m-30) REVERT: K 140 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8283 (mttm) REVERT: L 40 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8889 (mp) outliers start: 101 outliers final: 85 residues processed: 546 average time/residue: 0.2023 time to fit residues: 177.3741 Evaluate side-chains 568 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 475 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 367 optimal weight: 0.8980 chunk 311 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 338 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN C 172 GLN E 99 HIS F 78 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099469 restraints weight = 46254.435| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.76 r_work: 0.3023 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33169 Z= 0.128 Angle : 0.578 9.444 45142 Z= 0.303 Chirality : 0.044 0.202 5048 Planarity : 0.004 0.059 5572 Dihedral : 12.800 80.769 5032 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.53 % Allowed : 16.66 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3827 helix: 0.59 (0.15), residues: 1260 sheet: -0.91 (0.20), residues: 585 loop : -0.40 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 634 TYR 0.020 0.001 TYR A1104 PHE 0.018 0.001 PHE E 96 TRP 0.018 0.001 TRP B 836 HIS 0.008 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (33147) covalent geometry : angle 0.57501 / 0.30 (45121) hydrogen bonds : bond 0.03414 / 2.20 ( 1155) hydrogen bonds : angle 4.70848 / 3.23 ( 3232) metal coordination : bond 0.00375 / 0.23 ( 22) metal coordination : angle 2.61535 / 1.85 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 500 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8392 (tmm) cc_final: 0.7700 (ttp) REVERT: A 244 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7978 (ttt90) REVERT: A 393 SER cc_start: 0.8910 (m) cc_final: 0.8339 (p) REVERT: A 416 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6287 (ttm110) REVERT: A 423 LEU cc_start: 0.8493 (tp) cc_final: 0.8284 (tp) REVERT: A 490 ILE cc_start: 0.8643 (mm) cc_final: 0.8352 (mt) REVERT: A 604 LYS cc_start: 0.8628 (mttt) cc_final: 0.8356 (mtpt) REVERT: A 846 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9186 (mt) REVERT: A 1459 LYS cc_start: 0.8281 (tmtt) cc_final: 0.7685 (mtmt) REVERT: A 1471 GLU cc_start: 0.8202 (tp30) cc_final: 0.8001 (mm-30) REVERT: B 66 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: B 164 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8690 (ptp) REVERT: B 515 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7912 (t) REVERT: B 679 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7809 (mp10) REVERT: B 783 MET cc_start: 0.8430 (mtt) cc_final: 0.8016 (mtt) REVERT: B 785 ASP cc_start: 0.8724 (m-30) cc_final: 0.8418 (m-30) REVERT: B 944 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: C 174 ARG cc_start: 0.8093 (ptp-170) cc_final: 0.7796 (ptp90) REVERT: C 226 SER cc_start: 0.9010 (p) cc_final: 0.8807 (m) REVERT: C 319 ARG cc_start: 0.8831 (tpp80) cc_final: 0.8355 (mtt-85) REVERT: C 327 TYR cc_start: 0.8431 (t80) cc_final: 0.8054 (t80) REVERT: D 35 GLU cc_start: 0.8188 (mp0) cc_final: 0.7763 (mp0) REVERT: E 45 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8094 (ttpp) REVERT: E 122 LYS cc_start: 0.7895 (mmtp) cc_final: 0.6771 (pttm) REVERT: G 234 ARG cc_start: 0.6978 (ttt180) cc_final: 0.6553 (ttp-170) REVERT: H 27 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7860 (mt-10) REVERT: H 45 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7401 (tm-30) REVERT: H 86 ASP cc_start: 0.7943 (m-30) cc_final: 0.7705 (m-30) REVERT: H 133 ASN cc_start: 0.8493 (t0) cc_final: 0.8237 (m110) REVERT: K 85 ASP cc_start: 0.8571 (t0) cc_final: 0.8117 (t0) REVERT: K 97 SER cc_start: 0.9024 (m) cc_final: 0.8806 (m) REVERT: K 119 LYS cc_start: 0.8623 (tttt) cc_final: 0.8319 (tmtt) REVERT: K 126 ASP cc_start: 0.8573 (m-30) cc_final: 0.8365 (m-30) REVERT: K 140 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8275 (mttm) REVERT: L 40 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8927 (mp) outliers start: 87 outliers final: 73 residues processed: 554 average time/residue: 0.1959 time to fit residues: 175.3107 Evaluate side-chains 552 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 473 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 220 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 365 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1089 GLN F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097693 restraints weight = 46389.463| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.76 r_work: 0.2996 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33169 Z= 0.191 Angle : 0.611 9.232 45142 Z= 0.319 Chirality : 0.046 0.205 5048 Planarity : 0.004 0.061 5572 Dihedral : 12.806 81.796 5032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.77 % Allowed : 16.63 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3827 helix: 0.54 (0.15), residues: 1265 sheet: -0.84 (0.21), residues: 569 loop : -0.41 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 634 TYR 0.020 0.002 TYR A1302 PHE 0.017 0.002 PHE B1167 TRP 0.017 0.001 TRP B 836 HIS 0.009 0.001 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (33147) covalent geometry : angle 0.60848 / 0.32 (45121) hydrogen bonds : bond 0.03633 / 2.34 ( 1155) hydrogen bonds : angle 4.74893 / 3.26 ( 3232) metal coordination : bond 0.00569 / 0.36 ( 22) metal coordination : angle 2.87057 / 1.99 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9357.62 seconds wall clock time: 160 minutes 32.21 seconds (9632.21 seconds total)