Starting phenix.real_space_refine on Tue Aug 26 12:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.map" model { file = "/net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s54_19720/08_2025/8s54_19720.cif" } resolution = 3.4 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= 1.000 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 9 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 213 5.16 5 C 22874 2.51 5 N 6470 2.21 5 O 7084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 292 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36745 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1417, 11234 Classifications: {'peptide': 1417} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1346} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 9030 Classifications: {'peptide': 1130} Link IDs: {'PTRANS': 53, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 712 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "P" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1070 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 1 Chain: "T" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 70.719 106.614 73.512 1.00174.30 S ATOM 486 SG CYS A 74 67.215 105.001 73.230 1.00166.19 S ATOM 533 SG CYS A 81 70.279 102.840 74.014 1.00158.06 S ATOM 768 SG CYS A 111 73.487 72.732 36.916 1.00201.53 S ATOM 796 SG CYS A 114 70.122 74.647 35.329 1.00201.54 S ATOM 1142 SG CYS A 184 72.852 74.929 33.349 1.00226.25 S ATOM 19834 SG CYS B1119 56.933 94.474 64.993 1.00169.20 S ATOM 19856 SG CYS B1122 60.294 93.177 63.938 1.00164.56 S ATOM 19971 SG CYS B1137 59.805 96.931 64.699 1.00175.53 S ATOM 19992 SG CYS B1140 58.551 95.285 61.498 1.00181.61 S ATOM 20958 SG CYS C 88 85.131 106.998 138.557 1.00165.54 S ATOM 20971 SG CYS C 90 86.908 110.110 136.495 1.00172.25 S ATOM 21006 SG CYS C 94 88.443 108.889 139.417 1.00152.82 S ATOM 21028 SG CYS C 97 88.537 106.451 137.112 1.00150.06 S ATOM 28334 SG CYS I 17 129.307 41.932 42.796 1.00210.91 S ATOM 28358 SG CYS I 20 128.875 45.682 42.280 1.00217.22 S ATOM 28519 SG CYS I 39 125.741 43.409 42.198 1.00223.23 S ATOM 28544 SG CYS I 42 128.535 44.137 39.573 1.00228.49 S ATOM 28896 SG CYS I 86 133.985 27.715 84.841 1.00173.18 S ATOM 28920 SG CYS I 89 137.372 28.760 86.294 1.00174.18 S ATOM 29124 SG CYS I 114 134.502 31.225 86.451 1.00170.86 S ATOM 29159 SG CYS I 119 135.921 30.395 83.116 1.00180.01 S ATOM 29269 SG CYS J 7 103.321 78.489 130.234 1.00122.65 S ATOM 29293 SG CYS J 10 101.796 78.635 133.747 1.00120.81 S ATOM 29557 SG CYS J 44 103.215 75.435 132.412 1.00132.58 S ATOM 29563 SG CYS J 45 105.579 78.201 133.365 1.00134.20 S ATOM 30705 SG CYS L 19 119.066 112.158 106.464 1.00189.03 S ATOM 30724 SG CYS L 22 122.526 112.911 106.869 1.00194.64 S ATOM 30867 SG CYS L 39 122.439 112.027 103.384 1.00201.57 S ATOM 36198 SG CYS W 129 59.078 128.681 60.948 1.00413.16 S ATOM 36390 SG CYS W 154 60.151 126.113 64.581 1.00411.19 S ATOM 36414 SG CYS W 157 61.505 128.956 63.159 1.00414.39 S Time building chain proxies: 8.85, per 1000 atoms: 0.24 Number of scatterers: 36745 At special positions: 0 Unit cell: (179.55, 152.25, 172.2, 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 9 29.99 S 213 16.00 P 94 15.00 Mg 1 11.99 O 7084 8.00 N 6470 7.00 C 22874 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: 3.18 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " Number of angles added : 33 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8190 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 47 sheets defined 37.8% alpha, 14.9% beta 42 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.413A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.027A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.594A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.614A pdb=" N TYR A 242 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.698A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.582A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.617A pdb=" N ALA A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.613A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.882A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.747A pdb=" N ILE A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.582A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.824A pdb=" N ASN A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.540A pdb=" N VAL A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.759A pdb=" N GLY A 821 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.107A pdb=" N THR A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.530A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.731A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.743A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.710A pdb=" N PHE A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.518A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 4.964A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1047 " --> pdb=" O ILE A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.854A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.946A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.625A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 4.035A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 4.047A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 removed outlier: 3.707A pdb=" N ARG A1421 " --> pdb=" O GLY A1418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A1422 " --> pdb=" O VAL A1419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1418 through 1422' Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.682A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.730A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 4.047A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 247 through 253 removed outlier: 4.058A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.563A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.795A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.791A pdb=" N VAL B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.765A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 436 through 450 removed outlier: 4.435A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.575A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.889A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.517A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.502A pdb=" N MET B 702 " --> pdb=" O HIS B 699 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 704' Processing helix chain 'B' and resid 705 through 710 removed outlier: 4.169A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.762A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.712A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.562A pdb=" N LEU B1107 " --> pdb=" O LEU B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.519A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.596A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 271 removed outlier: 3.977A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.768A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 4.130A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.588A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.860A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.588A pdb=" N GLN D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.544A pdb=" N PHE E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 98 removed outlier: 3.535A pdb=" N MET E 94 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN E 95 " --> pdb=" O CYS E 91 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.562A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.622A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.882A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.627A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.544A pdb=" N GLU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5 through 10' Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.564A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.817A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 161 through 165 removed outlier: 3.902A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 175 through 180 removed outlier: 3.818A pdb=" N GLN Q 179 " --> pdb=" O SER Q 175 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 175 through 180' Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 24 through 35 removed outlier: 3.582A pdb=" N SER R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.629A pdb=" N ASN R 64 " --> pdb=" O GLU R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 136 removed outlier: 4.277A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 130 " --> pdb=" O ARG R 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 25 removed outlier: 3.771A pdb=" N LYS W 15 " --> pdb=" O PRO W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 40 removed outlier: 3.787A pdb=" N ILE W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 53 Processing helix chain 'W' and resid 55 through 69 Processing helix chain 'W' and resid 95 through 124 removed outlier: 3.686A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 144 Processing helix chain 'W' and resid 163 through 167 Processing helix chain 'W' and resid 168 through 184 removed outlier: 4.342A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.623A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 3.518A pdb=" N LEU A 253 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 90 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.643A pdb=" N GLU A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.667A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.715A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.316A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 59 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG H 57 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN H 126 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 116 " --> pdb=" O MET H 123 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.950A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.906A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB2, first strand: chain 'A' and resid 1140 through 1142 removed outlier: 4.092A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.890A pdb=" N ARG A1258 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1319 through 1321 removed outlier: 4.124A pdb=" N ILE A1321 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.970A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 67 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 87 current: chain 'B' and resid 121 through 133 removed outlier: 6.365A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.677A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC2, first strand: chain 'B' and resid 208 through 209 removed outlier: 5.018A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 257 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.629A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.639A pdb=" N GLU B 551 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 576 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 628 through 629 Processing sheet with id=AC6, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.703A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.235A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B1048 " --> pdb=" O ILE B 776 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 815 through 817 removed outlier: 3.511A pdb=" N GLU B 816 " --> pdb=" O CYS B 919 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 919 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 827 through 829 removed outlier: 3.683A pdb=" N THR B 870 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.668A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD4, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.614A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 24 current: chain 'C' and resid 229 through 231 Processing sheet with id=AD5, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.967A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 50 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.914A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.899A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 101 through 106 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 3 through 13 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 7.024A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 117 through 120 removed outlier: 4.432A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AE6, first strand: chain 'I' and resid 94 through 97 removed outlier: 3.535A pdb=" N PHE I 97 " --> pdb=" O TYR I 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 21 through 22 Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 17 current: chain 'Q' and resid 134 through 139 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 134 through 139 current: chain 'R' and resid 52 through 58 removed outlier: 10.089A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 86 current: chain 'R' and resid 104 through 116 Processing sheet with id=AE9, first strand: chain 'Q' and resid 45 through 46 removed outlier: 4.333A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 42 through 44 Processing sheet with id=AF2, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.607A pdb=" N PHE W 127 " --> pdb=" O PHE W 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 11.16 Time building geometry restraints manager: 4.29 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: 8125 1.33 - 1.45: 8397 1.45 - 1.58: 20581 1.58 - 1.70: 186 1.70 - 1.82: 336 Bond restraints: 37625 Sorted by residual: bond pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N LEU A 236 " pdb=" CA LEU A 236 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 bond pdb=" CZ ARG B1085 " pdb=" NH2 ARG B1085 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.86e+00 bond pdb=" N GLY B1077 " pdb=" CA GLY B1077 " ideal model delta sigma weight residual 1.447 1.474 -0.027 9.90e-03 1.02e+04 7.52e+00 bond pdb=" CZ ARG A 358 " pdb=" NH2 ARG A 358 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.45e+00 ... (remaining 37620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 49791 2.76 - 5.51: 1161 5.51 - 8.27: 234 8.27 - 11.03: 23 11.03 - 13.78: 6 Bond angle restraints: 51215 Sorted by residual: angle pdb=" N GLN A 539 " pdb=" CA GLN A 539 " pdb=" C GLN A 539 " ideal model delta sigma weight residual 110.80 121.73 -10.93 2.13e+00 2.20e-01 2.64e+01 angle pdb=" C ASN B 649 " pdb=" N ASN B 650 " pdb=" CA ASN B 650 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" CA HIS B1060 " pdb=" CB HIS B1060 " pdb=" CG HIS B1060 " ideal model delta sigma weight residual 113.80 109.01 4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" O3' DA T 59 " pdb=" P DG T 60 " pdb=" O5' DG T 60 " ideal model delta sigma weight residual 104.00 96.97 7.03 1.50e+00 4.44e-01 2.19e+01 angle pdb=" CB MET A 561 " pdb=" CG MET A 561 " pdb=" SD MET A 561 " ideal model delta sigma weight residual 112.70 98.92 13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 51210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 22184 35.28 - 70.56: 612 70.56 - 105.85: 35 105.85 - 141.13: 1 141.13 - 176.41: 3 Dihedral angle restraints: 22835 sinusoidal: 10186 harmonic: 12649 Sorted by residual: dihedral pdb=" C GLU A1434 " pdb=" N GLU A1434 " pdb=" CA GLU A1434 " pdb=" CB GLU A1434 " ideal model delta harmonic sigma weight residual -122.60 -136.33 13.73 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" CA GLN A1101 " pdb=" C GLN A1101 " pdb=" N MET A1102 " pdb=" CA MET A1102 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA GLN A 330 " pdb=" C GLN A 330 " pdb=" N LYS A 331 " pdb=" CA LYS A 331 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 22832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 5481 0.127 - 0.255: 144 0.255 - 0.382: 10 0.382 - 0.509: 16 0.509 - 0.637: 67 Chirality restraints: 5718 Sorted by residual: chirality pdb=" P DT N 57 " pdb=" OP1 DT N 57 " pdb=" OP2 DT N 57 " pdb=" O5' DT N 57 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DG T 28 " pdb=" OP1 DG T 28 " pdb=" OP2 DG T 28 " pdb=" O5' DG T 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DT T 21 " pdb=" OP1 DT T 21 " pdb=" OP2 DT T 21 " pdb=" O5' DT T 21 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 5715 not shown) Planarity restraints: 6309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG N 69 " 0.079 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" N9 DG N 69 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DG N 69 " -0.080 2.00e-02 2.50e+03 pdb=" N7 DG N 69 " -0.089 2.00e-02 2.50e+03 pdb=" C5 DG N 69 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DG N 69 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG N 69 " 0.068 2.00e-02 2.50e+03 pdb=" N1 DG N 69 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DG N 69 " 0.021 2.00e-02 2.50e+03 pdb=" N2 DG N 69 " -0.116 2.00e-02 2.50e+03 pdb=" N3 DG N 69 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG N 69 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 64 " 0.082 2.00e-02 2.50e+03 5.73e-02 9.87e+01 pdb=" N9 DG N 64 " 0.050 2.00e-02 2.50e+03 pdb=" C8 DG N 64 " -0.086 2.00e-02 2.50e+03 pdb=" N7 DG N 64 " -0.086 2.00e-02 2.50e+03 pdb=" C5 DG N 64 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG N 64 " 0.019 2.00e-02 2.50e+03 pdb=" O6 DG N 64 " 0.100 2.00e-02 2.50e+03 pdb=" N1 DG N 64 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG N 64 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG N 64 " -0.067 2.00e-02 2.50e+03 pdb=" N3 DG N 64 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG N 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 74 " 0.058 2.00e-02 2.50e+03 4.74e-02 6.75e+01 pdb=" N9 DG N 74 " 0.014 2.00e-02 2.50e+03 pdb=" C8 DG N 74 " -0.085 2.00e-02 2.50e+03 pdb=" N7 DG N 74 " -0.056 2.00e-02 2.50e+03 pdb=" C5 DG N 74 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG N 74 " 0.027 2.00e-02 2.50e+03 pdb=" O6 DG N 74 " 0.057 2.00e-02 2.50e+03 pdb=" N1 DG N 74 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG N 74 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG N 74 " -0.084 2.00e-02 2.50e+03 pdb=" N3 DG N 74 " 0.039 2.00e-02 2.50e+03 pdb=" C4 DG N 74 " 0.025 2.00e-02 2.50e+03 ... (remaining 6306 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 4 2.20 - 2.87: 12472 2.87 - 3.55: 51806 3.55 - 4.22: 85599 4.22 - 4.90: 142482 Nonbonded interactions: 292363 Sorted by model distance: nonbonded pdb=" NH1 ARG A 862 " pdb=" OE1 GLU B1088 " model vdw 1.522 3.120 nonbonded pdb=" O3' A P 14 " pdb="MG MG P 101 " model vdw 1.531 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG P 101 " model vdw 2.069 2.170 nonbonded pdb=" NE ARG A 351 " pdb=" NH2 ARG A 862 " model vdw 2.147 3.200 nonbonded pdb=" OG1 THR B 474 " pdb=" O ALA B 732 " model vdw 2.224 3.040 ... (remaining 292358 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 45.690 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.006 0.698 37658 Z= 0.284 Angle : 1.005 24.246 51248 Z= 0.512 Chirality : 0.085 0.637 5718 Planarity : 0.009 0.280 6309 Dihedral : 15.632 176.412 14645 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.12), residues: 4291 helix: -1.00 (0.12), residues: 1482 sheet: -0.28 (0.22), residues: 593 loop : -1.36 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1396 TYR 0.054 0.002 TYR A 145 PHE 0.044 0.002 PHE B1086 TRP 0.017 0.002 TRP A1192 HIS 0.015 0.001 HIS B 970 Details of bonding type rmsd covalent geometry : bond 0.00524 (37625) covalent geometry : angle 0.99017 (51215) hydrogen bonds : bond 0.19726 ( 1404) hydrogen bonds : angle 7.48825 ( 3850) metal coordination : bond 0.12169 ( 33) metal coordination : angle 6.92937 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 791 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8274 (t70) cc_final: 0.8027 (t0) REVERT: A 109 CYS cc_start: 0.9515 (t) cc_final: 0.9164 (t) REVERT: A 139 LYS cc_start: 0.7716 (tttt) cc_final: 0.7093 (mmmt) REVERT: A 219 GLU cc_start: 0.8714 (tp30) cc_final: 0.8481 (tp30) REVERT: A 274 ASP cc_start: 0.8704 (t70) cc_final: 0.8496 (t70) REVERT: A 319 ASP cc_start: 0.8750 (t0) cc_final: 0.8417 (t0) REVERT: A 322 LEU cc_start: 0.8931 (mt) cc_final: 0.8706 (mt) REVERT: A 470 MET cc_start: 0.9043 (ptt) cc_final: 0.8607 (ptt) REVERT: A 496 PHE cc_start: 0.8246 (m-10) cc_final: 0.7723 (m-10) REVERT: A 747 ASP cc_start: 0.8904 (t0) cc_final: 0.8646 (t0) REVERT: A 870 SER cc_start: 0.9239 (p) cc_final: 0.8995 (p) REVERT: A 1196 TYR cc_start: 0.8978 (t80) cc_final: 0.8631 (t80) REVERT: A 1210 TRP cc_start: 0.8789 (m100) cc_final: 0.8488 (m100) REVERT: A 1353 ASP cc_start: 0.8901 (t0) cc_final: 0.8588 (t0) REVERT: A 1434 GLU cc_start: 0.8682 (pt0) cc_final: 0.8382 (pt0) REVERT: B 208 PHE cc_start: 0.8290 (m-80) cc_final: 0.7860 (m-80) REVERT: B 382 LEU cc_start: 0.8903 (mm) cc_final: 0.8591 (mm) REVERT: B 384 ASP cc_start: 0.7916 (t0) cc_final: 0.7646 (t70) REVERT: B 508 MET cc_start: 0.8395 (mmp) cc_final: 0.8190 (mmp) REVERT: B 563 ASP cc_start: 0.8355 (t70) cc_final: 0.8141 (t0) REVERT: B 579 ASP cc_start: 0.8353 (t0) cc_final: 0.7874 (t0) REVERT: B 668 LEU cc_start: 0.8133 (mm) cc_final: 0.7804 (mm) REVERT: B 764 MET cc_start: 0.8301 (ptp) cc_final: 0.8094 (ptp) REVERT: B 789 ASN cc_start: 0.7980 (p0) cc_final: 0.7369 (p0) REVERT: B 854 ILE cc_start: 0.9249 (tp) cc_final: 0.9020 (tp) REVERT: B 1089 MET cc_start: 0.8554 (mtm) cc_final: 0.8301 (mtm) REVERT: B 1092 ASP cc_start: 0.8733 (m-30) cc_final: 0.8466 (m-30) REVERT: B 1093 CYS cc_start: 0.7977 (t) cc_final: 0.7372 (t) REVERT: B 1151 MET cc_start: 0.8921 (ptm) cc_final: 0.8095 (tmm) REVERT: C 83 GLN cc_start: 0.9051 (mt0) cc_final: 0.8776 (mt0) REVERT: C 265 HIS cc_start: 0.8639 (t-90) cc_final: 0.8296 (t-90) REVERT: D 71 PHE cc_start: 0.4677 (m-80) cc_final: 0.4215 (m-80) REVERT: E 44 PHE cc_start: 0.8765 (m-10) cc_final: 0.8331 (m-10) REVERT: E 94 MET cc_start: 0.9536 (mmp) cc_final: 0.8357 (mmm) REVERT: E 98 ASN cc_start: 0.9466 (t0) cc_final: 0.9165 (p0) REVERT: E 108 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8627 (tm-30) REVERT: E 129 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7915 (tm-30) REVERT: F 115 TYR cc_start: 0.8534 (p90) cc_final: 0.7963 (p90) REVERT: F 117 ASP cc_start: 0.8309 (m-30) cc_final: 0.8018 (m-30) REVERT: G 52 ASP cc_start: 0.8400 (t70) cc_final: 0.8131 (t70) REVERT: H 48 TYR cc_start: 0.8288 (t80) cc_final: 0.7828 (t80) REVERT: H 74 GLU cc_start: 0.8522 (mp0) cc_final: 0.8317 (mp0) REVERT: H 76 ASN cc_start: 0.8716 (m110) cc_final: 0.8410 (m110) REVERT: H 123 MET cc_start: 0.8999 (ptt) cc_final: 0.8398 (ptt) REVERT: I 36 LEU cc_start: 0.8490 (tp) cc_final: 0.8204 (tp) REVERT: I 46 GLN cc_start: 0.8164 (pm20) cc_final: 0.7957 (pm20) REVERT: I 47 GLU cc_start: 0.8719 (pp20) cc_final: 0.8409 (pp20) REVERT: I 83 ASP cc_start: 0.8738 (p0) cc_final: 0.8148 (p0) REVERT: I 84 HIS cc_start: 0.8669 (m170) cc_final: 0.8339 (m170) REVERT: I 121 HIS cc_start: 0.8719 (t-170) cc_final: 0.8408 (t-170) REVERT: J 16 ASN cc_start: 0.8860 (p0) cc_final: 0.8613 (p0) REVERT: K 2 ASN cc_start: 0.8647 (m110) cc_final: 0.8369 (m110) REVERT: K 31 CYS cc_start: 0.7893 (t) cc_final: 0.7645 (t) REVERT: L 42 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7690 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 791 average time/residue: 0.2229 time to fit residues: 297.7990 Evaluate side-chains 632 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 30.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 293 ASN A 341 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 601 ASN A 703 GLN A 861 GLN A 904 GLN A1032 GLN A1163 HIS ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 98 HIS B 111 ASN B 139 GLN B 265 GLN B 344 GLN B 654 GLN B 683 GLN B 716 HIS B 731 GLN B 930 GLN B1021 HIS B1097 HIS B1120 ASN C 51 GLN C 194 HIS C 217 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS H 126 GLN I 60 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS K 2 ASN Q 32 ASN Q 53 ASN R 152 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.138132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084217 restraints weight = 71380.779| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.15 r_work: 0.2892 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37658 Z= 0.143 Angle : 0.639 17.663 51248 Z= 0.328 Chirality : 0.044 0.177 5718 Planarity : 0.005 0.056 6309 Dihedral : 13.895 177.670 5820 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.86 % Allowed : 9.57 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.13), residues: 4291 helix: 0.08 (0.13), residues: 1498 sheet: -0.26 (0.21), residues: 597 loop : -1.14 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 44 TYR 0.027 0.001 TYR B 262 PHE 0.019 0.001 PHE E 73 TRP 0.010 0.001 TRP C 49 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00319 (37625) covalent geometry : angle 0.62554 (51215) hydrogen bonds : bond 0.04459 ( 1404) hydrogen bonds : angle 5.18761 ( 3850) metal coordination : bond 0.00688 ( 33) metal coordination : angle 5.23296 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 684 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9613 (t) cc_final: 0.9340 (t) REVERT: A 274 ASP cc_start: 0.8500 (t70) cc_final: 0.8197 (t70) REVERT: A 317 MET cc_start: 0.9016 (tmm) cc_final: 0.8742 (tmm) REVERT: A 319 ASP cc_start: 0.9042 (t0) cc_final: 0.8839 (t0) REVERT: A 341 GLN cc_start: 0.9024 (mm110) cc_final: 0.8680 (mm-40) REVERT: A 370 ASP cc_start: 0.9207 (t70) cc_final: 0.8967 (t70) REVERT: A 376 ASP cc_start: 0.8500 (p0) cc_final: 0.8261 (p0) REVERT: A 470 MET cc_start: 0.8971 (ptt) cc_final: 0.8584 (ptt) REVERT: A 561 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: A 683 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 868 MET cc_start: 0.8072 (mmp) cc_final: 0.7533 (mmm) REVERT: A 870 SER cc_start: 0.9371 (p) cc_final: 0.9124 (t) REVERT: A 982 ASN cc_start: 0.8281 (t0) cc_final: 0.7972 (t0) REVERT: A 1192 TRP cc_start: 0.8687 (p90) cc_final: 0.7991 (p90) REVERT: A 1196 TYR cc_start: 0.9200 (t80) cc_final: 0.8957 (t80) REVERT: A 1284 PHE cc_start: 0.7823 (t80) cc_final: 0.7389 (t80) REVERT: A 1351 ASP cc_start: 0.9103 (m-30) cc_final: 0.8728 (m-30) REVERT: A 1353 ASP cc_start: 0.9057 (t0) cc_final: 0.8585 (t0) REVERT: A 1428 MET cc_start: 0.9114 (tmm) cc_final: 0.8751 (tmm) REVERT: A 1434 GLU cc_start: 0.9096 (pt0) cc_final: 0.8721 (pt0) REVERT: B 108 MET cc_start: 0.9321 (ttm) cc_final: 0.8860 (ttp) REVERT: B 206 TYR cc_start: 0.8448 (m-10) cc_final: 0.8164 (m-10) REVERT: B 208 PHE cc_start: 0.8542 (m-80) cc_final: 0.7966 (m-10) REVERT: B 345 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7072 (ttmt) REVERT: B 382 LEU cc_start: 0.8976 (mm) cc_final: 0.8354 (mm) REVERT: B 438 ARG cc_start: 0.7532 (tpm170) cc_final: 0.7221 (tpm170) REVERT: B 563 ASP cc_start: 0.8812 (t70) cc_final: 0.8585 (t0) REVERT: B 579 ASP cc_start: 0.8354 (t0) cc_final: 0.7865 (t0) REVERT: B 671 GLU cc_start: 0.9058 (tp30) cc_final: 0.8833 (mt-10) REVERT: B 767 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 789 ASN cc_start: 0.8515 (p0) cc_final: 0.7887 (p0) REVERT: B 854 ILE cc_start: 0.9331 (tp) cc_final: 0.9102 (tp) REVERT: B 906 GLN cc_start: 0.8694 (tt0) cc_final: 0.8336 (pt0) REVERT: B 910 THR cc_start: 0.9480 (t) cc_final: 0.9149 (m) REVERT: B 1088 GLU cc_start: 0.8122 (mp0) cc_final: 0.7639 (mp0) REVERT: B 1092 ASP cc_start: 0.9169 (m-30) cc_final: 0.8805 (m-30) REVERT: C 83 GLN cc_start: 0.9251 (mt0) cc_final: 0.8938 (mt0) REVERT: C 265 HIS cc_start: 0.8813 (t-90) cc_final: 0.8507 (t-90) REVERT: E 79 GLU cc_start: 0.8898 (mp0) cc_final: 0.8415 (pm20) REVERT: E 94 MET cc_start: 0.9415 (mmp) cc_final: 0.8783 (mmm) REVERT: E 108 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8795 (tm-30) REVERT: E 138 ASN cc_start: 0.8076 (t0) cc_final: 0.7828 (t0) REVERT: E 177 ASP cc_start: 0.9256 (t0) cc_final: 0.8984 (t70) REVERT: F 61 GLU cc_start: 0.9047 (pm20) cc_final: 0.8678 (pm20) REVERT: F 115 TYR cc_start: 0.8963 (p90) cc_final: 0.8413 (p90) REVERT: H 74 GLU cc_start: 0.8735 (mp0) cc_final: 0.8464 (mp0) REVERT: H 89 GLU cc_start: 0.8215 (pp20) cc_final: 0.7551 (pp20) REVERT: H 118 TYR cc_start: 0.9384 (m-80) cc_final: 0.9119 (m-80) REVERT: I 36 LEU cc_start: 0.8134 (tp) cc_final: 0.7933 (tp) REVERT: I 47 GLU cc_start: 0.8992 (pp20) cc_final: 0.8645 (pp20) REVERT: I 83 ASP cc_start: 0.8761 (p0) cc_final: 0.8220 (p0) REVERT: I 84 HIS cc_start: 0.8826 (m170) cc_final: 0.8407 (m170) REVERT: I 121 HIS cc_start: 0.8824 (t-170) cc_final: 0.8395 (t-170) REVERT: J 16 ASN cc_start: 0.9102 (p0) cc_final: 0.8840 (p0) REVERT: K 2 ASN cc_start: 0.8924 (m-40) cc_final: 0.8560 (m110) REVERT: K 24 ASP cc_start: 0.8704 (t0) cc_final: 0.8441 (t0) REVERT: K 31 CYS cc_start: 0.8359 (t) cc_final: 0.8053 (t) REVERT: L 44 MET cc_start: 0.7263 (mmt) cc_final: 0.6945 (mmt) outliers start: 33 outliers final: 24 residues processed: 697 average time/residue: 0.2220 time to fit residues: 262.8274 Evaluate side-chains 655 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 629 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 55 optimal weight: 2.9990 chunk 236 optimal weight: 0.0770 chunk 14 optimal weight: 10.0000 chunk 303 optimal weight: 0.0970 chunk 306 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 390 optimal weight: 40.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN A 620 HIS A 804 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1230 GLN ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN B 111 ASN B 139 GLN B 817 GLN B 930 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 46 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN Q 178 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083205 restraints weight = 71415.028| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.12 r_work: 0.2870 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37658 Z= 0.139 Angle : 0.609 16.199 51248 Z= 0.310 Chirality : 0.044 0.180 5718 Planarity : 0.004 0.052 6309 Dihedral : 13.811 177.696 5820 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.38 % Allowed : 12.74 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 4291 helix: 0.54 (0.14), residues: 1501 sheet: -0.23 (0.21), residues: 625 loop : -1.02 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1396 TYR 0.021 0.001 TYR E 90 PHE 0.024 0.001 PHE L 55 TRP 0.012 0.001 TRP C 49 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00316 (37625) covalent geometry : angle 0.59778 (51215) hydrogen bonds : bond 0.03694 ( 1404) hydrogen bonds : angle 4.75435 ( 3850) metal coordination : bond 0.00584 ( 33) metal coordination : angle 4.53576 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 677 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7987 (pm20) cc_final: 0.7612 (pm20) REVERT: A 109 CYS cc_start: 0.9564 (t) cc_final: 0.9271 (t) REVERT: A 274 ASP cc_start: 0.8467 (t70) cc_final: 0.8155 (t70) REVERT: A 317 MET cc_start: 0.8972 (tmm) cc_final: 0.8658 (tmm) REVERT: A 370 ASP cc_start: 0.9148 (t70) cc_final: 0.8735 (t70) REVERT: A 470 MET cc_start: 0.8952 (ptt) cc_final: 0.8457 (ptt) REVERT: A 483 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8104 (mpp80) REVERT: A 496 PHE cc_start: 0.8658 (m-10) cc_final: 0.7953 (m-10) REVERT: A 561 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8751 (mmm) REVERT: A 634 GLU cc_start: 0.8061 (tp30) cc_final: 0.7673 (mm-30) REVERT: A 683 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 870 SER cc_start: 0.9344 (p) cc_final: 0.9123 (t) REVERT: A 962 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9025 (t0) REVERT: A 982 ASN cc_start: 0.8362 (t0) cc_final: 0.8107 (t0) REVERT: A 1005 HIS cc_start: 0.7539 (t70) cc_final: 0.7279 (t-90) REVERT: A 1192 TRP cc_start: 0.8687 (p90) cc_final: 0.8091 (p90) REVERT: A 1196 TYR cc_start: 0.9234 (t80) cc_final: 0.9029 (t80) REVERT: A 1210 TRP cc_start: 0.8733 (m100) cc_final: 0.8373 (m100) REVERT: A 1284 PHE cc_start: 0.7828 (t80) cc_final: 0.7507 (t80) REVERT: A 1293 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9222 (mm) REVERT: A 1351 ASP cc_start: 0.9142 (m-30) cc_final: 0.8744 (m-30) REVERT: A 1353 ASP cc_start: 0.9082 (t0) cc_final: 0.8593 (t0) REVERT: A 1428 MET cc_start: 0.9086 (tmm) cc_final: 0.8754 (tmm) REVERT: A 1434 GLU cc_start: 0.9055 (pt0) cc_final: 0.8658 (pt0) REVERT: B 108 MET cc_start: 0.9334 (ttm) cc_final: 0.9033 (ttp) REVERT: B 155 MET cc_start: 0.8386 (ptt) cc_final: 0.8179 (ptt) REVERT: B 206 TYR cc_start: 0.8122 (m-10) cc_final: 0.7859 (m-10) REVERT: B 208 PHE cc_start: 0.8463 (m-80) cc_final: 0.7817 (m-10) REVERT: B 239 MET cc_start: 0.6792 (mmm) cc_final: 0.6566 (mmm) REVERT: B 345 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7160 (ttmt) REVERT: B 438 ARG cc_start: 0.7591 (tpm170) cc_final: 0.7207 (tpm170) REVERT: B 508 MET cc_start: 0.9267 (mmp) cc_final: 0.8285 (mmp) REVERT: B 563 ASP cc_start: 0.8808 (t70) cc_final: 0.8552 (t0) REVERT: B 579 ASP cc_start: 0.8349 (t0) cc_final: 0.7864 (t0) REVERT: B 671 GLU cc_start: 0.9097 (tp30) cc_final: 0.8831 (tp30) REVERT: B 751 LEU cc_start: 0.9358 (tt) cc_final: 0.8975 (tt) REVERT: B 767 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8907 (mp) REVERT: B 789 ASN cc_start: 0.8552 (p0) cc_final: 0.7772 (p0) REVERT: B 854 ILE cc_start: 0.9323 (tp) cc_final: 0.9104 (tp) REVERT: B 906 GLN cc_start: 0.8748 (tt0) cc_final: 0.8248 (pt0) REVERT: B 910 THR cc_start: 0.9426 (t) cc_final: 0.9002 (m) REVERT: B 990 SER cc_start: 0.9625 (t) cc_final: 0.9362 (p) REVERT: B 1088 GLU cc_start: 0.8031 (mp0) cc_final: 0.7592 (mp0) REVERT: B 1092 ASP cc_start: 0.9187 (m-30) cc_final: 0.8832 (m-30) REVERT: C 83 GLN cc_start: 0.9256 (mt0) cc_final: 0.8947 (mt0) REVERT: C 265 HIS cc_start: 0.8791 (t-90) cc_final: 0.8474 (t-90) REVERT: E 79 GLU cc_start: 0.8869 (mp0) cc_final: 0.8265 (pm20) REVERT: E 94 MET cc_start: 0.9430 (mmp) cc_final: 0.8950 (mmm) REVERT: E 108 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8809 (tm-30) REVERT: E 138 ASN cc_start: 0.8135 (t0) cc_final: 0.7773 (t0) REVERT: F 115 TYR cc_start: 0.8914 (p90) cc_final: 0.8385 (p90) REVERT: G 60 GLN cc_start: 0.8556 (mm110) cc_final: 0.8142 (mt0) REVERT: H 8 ASP cc_start: 0.7305 (t0) cc_final: 0.7099 (t0) REVERT: H 75 TYR cc_start: 0.9264 (t80) cc_final: 0.9033 (t80) REVERT: H 89 GLU cc_start: 0.8201 (pp20) cc_final: 0.7455 (pp20) REVERT: I 23 MET cc_start: 0.8104 (tpp) cc_final: 0.7869 (tpp) REVERT: I 45 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8488 (mm110) REVERT: I 47 GLU cc_start: 0.9040 (pp20) cc_final: 0.8687 (pp20) REVERT: I 69 ILE cc_start: 0.9342 (mm) cc_final: 0.8978 (mm) REVERT: I 83 ASP cc_start: 0.8700 (p0) cc_final: 0.8173 (p0) REVERT: I 84 HIS cc_start: 0.8866 (m170) cc_final: 0.8427 (m170) REVERT: I 121 HIS cc_start: 0.8826 (t-170) cc_final: 0.8434 (t-170) REVERT: J 16 ASN cc_start: 0.9115 (p0) cc_final: 0.8871 (p0) REVERT: J 33 ASP cc_start: 0.9182 (m-30) cc_final: 0.8637 (p0) REVERT: K 2 ASN cc_start: 0.8987 (m-40) cc_final: 0.8620 (m110) REVERT: K 24 ASP cc_start: 0.8688 (t0) cc_final: 0.8245 (t0) REVERT: K 27 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8978 (p) REVERT: K 29 ASN cc_start: 0.9055 (m-40) cc_final: 0.8619 (p0) REVERT: K 31 CYS cc_start: 0.8340 (t) cc_final: 0.7885 (t) REVERT: K 53 ASP cc_start: 0.9164 (t0) cc_final: 0.8855 (t0) REVERT: L 44 MET cc_start: 0.7860 (mmt) cc_final: 0.7512 (mmt) outliers start: 53 outliers final: 35 residues processed: 693 average time/residue: 0.2190 time to fit residues: 258.4499 Evaluate side-chains 657 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 617 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 250 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 296 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN B 503 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN I 46 GLN ** I 74 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 = 0.3921 r_free = 0.3921 target = 0.135406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.082015 restraints weight = 71147.484| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.12 r_work: 0.2847 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37658 Z= 0.139 Angle : 0.597 15.297 51248 Z= 0.303 Chirality : 0.043 0.184 5718 Planarity : 0.004 0.055 6309 Dihedral : 13.767 178.681 5820 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.87 % Allowed : 14.66 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.13), residues: 4291 helix: 0.79 (0.14), residues: 1502 sheet: -0.22 (0.21), residues: 625 loop : -0.95 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 69 TYR 0.023 0.001 TYR I 44 PHE 0.028 0.001 PHE L 55 TRP 0.011 0.001 TRP C 49 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00321 (37625) covalent geometry : angle 0.58717 (51215) hydrogen bonds : bond 0.03412 ( 1404) hydrogen bonds : angle 4.55308 ( 3850) metal coordination : bond 0.00555 ( 33) metal coordination : angle 4.18563 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 661 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7952 (pm20) cc_final: 0.7563 (pm20) REVERT: A 62 GLN cc_start: 0.9443 (tp-100) cc_final: 0.9053 (mm-40) REVERT: A 109 CYS cc_start: 0.9566 (t) cc_final: 0.9270 (t) REVERT: A 274 ASP cc_start: 0.8485 (t70) cc_final: 0.8159 (t70) REVERT: A 317 MET cc_start: 0.8948 (tmm) cc_final: 0.8244 (tmm) REVERT: A 337 LYS cc_start: 0.8245 (tptp) cc_final: 0.8004 (tptp) REVERT: A 470 MET cc_start: 0.9017 (ptt) cc_final: 0.8505 (ptt) REVERT: A 496 PHE cc_start: 0.8703 (m-10) cc_final: 0.7784 (m-10) REVERT: A 501 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: A 631 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: A 634 GLU cc_start: 0.8012 (tp30) cc_final: 0.7710 (mm-30) REVERT: A 683 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 850 THR cc_start: 0.8585 (t) cc_final: 0.8379 (p) REVERT: A 962 ASP cc_start: 0.9499 (OUTLIER) cc_final: 0.8963 (t0) REVERT: A 982 ASN cc_start: 0.8446 (t0) cc_final: 0.8132 (t0) REVERT: A 1192 TRP cc_start: 0.8712 (p90) cc_final: 0.8074 (p90) REVERT: A 1210 TRP cc_start: 0.8729 (m100) cc_final: 0.8438 (m100) REVERT: A 1293 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9225 (mm) REVERT: A 1353 ASP cc_start: 0.9078 (t0) cc_final: 0.8570 (t0) REVERT: A 1428 MET cc_start: 0.9056 (tmm) cc_final: 0.8782 (tmm) REVERT: A 1434 GLU cc_start: 0.9006 (pt0) cc_final: 0.8651 (pt0) REVERT: B 53 MET cc_start: 0.8879 (mmp) cc_final: 0.8628 (mmm) REVERT: B 108 MET cc_start: 0.9294 (ttm) cc_final: 0.8933 (ttp) REVERT: B 206 TYR cc_start: 0.8080 (m-10) cc_final: 0.7850 (m-10) REVERT: B 208 PHE cc_start: 0.8501 (m-80) cc_final: 0.7893 (m-10) REVERT: B 422 PHE cc_start: 0.8227 (t80) cc_final: 0.7893 (t80) REVERT: B 508 MET cc_start: 0.9328 (mmp) cc_final: 0.7968 (mmp) REVERT: B 563 ASP cc_start: 0.8819 (t70) cc_final: 0.8555 (t0) REVERT: B 579 ASP cc_start: 0.8385 (t0) cc_final: 0.7868 (t0) REVERT: B 751 LEU cc_start: 0.9352 (tt) cc_final: 0.8925 (tt) REVERT: B 789 ASN cc_start: 0.8584 (p0) cc_final: 0.7855 (p0) REVERT: B 840 MET cc_start: 0.4864 (mmp) cc_final: 0.2394 (ttm) REVERT: B 854 ILE cc_start: 0.9325 (tp) cc_final: 0.9115 (tp) REVERT: B 910 THR cc_start: 0.9396 (t) cc_final: 0.8966 (m) REVERT: B 990 SER cc_start: 0.9627 (t) cc_final: 0.9372 (p) REVERT: B 1048 TYR cc_start: 0.9046 (m-80) cc_final: 0.8752 (m-80) REVERT: C 83 GLN cc_start: 0.9251 (mt0) cc_final: 0.8929 (mt0) REVERT: C 265 HIS cc_start: 0.8752 (t-90) cc_final: 0.8481 (t-90) REVERT: D 44 ARG cc_start: 0.9120 (tpt-90) cc_final: 0.8777 (tpt-90) REVERT: E 79 GLU cc_start: 0.8938 (mp0) cc_final: 0.8356 (pm20) REVERT: E 82 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8090 (m) REVERT: E 92 GLN cc_start: 0.8595 (mm110) cc_final: 0.8356 (mm-40) REVERT: E 94 MET cc_start: 0.9424 (mmp) cc_final: 0.8852 (mmm) REVERT: E 108 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8812 (tm-30) REVERT: E 120 ASP cc_start: 0.7802 (p0) cc_final: 0.7600 (p0) REVERT: E 138 ASN cc_start: 0.8216 (t0) cc_final: 0.7818 (t0) REVERT: E 177 ASP cc_start: 0.9203 (t0) cc_final: 0.8754 (t70) REVERT: F 61 GLU cc_start: 0.9287 (pm20) cc_final: 0.9027 (pm20) REVERT: F 115 TYR cc_start: 0.8938 (p90) cc_final: 0.8430 (p90) REVERT: G 60 GLN cc_start: 0.8553 (mm110) cc_final: 0.8069 (mt0) REVERT: H 7 GLU cc_start: 0.8353 (tp30) cc_final: 0.8124 (tp30) REVERT: H 31 GLU cc_start: 0.8093 (pm20) cc_final: 0.7769 (pm20) REVERT: H 74 GLU cc_start: 0.8685 (mp0) cc_final: 0.8347 (mp0) REVERT: H 75 TYR cc_start: 0.9319 (t80) cc_final: 0.9061 (t80) REVERT: H 89 GLU cc_start: 0.8184 (pp20) cc_final: 0.7374 (pp20) REVERT: H 126 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.6983 (mp-120) REVERT: I 20 CYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8711 (p) REVERT: I 47 GLU cc_start: 0.8946 (pp20) cc_final: 0.8553 (pp20) REVERT: I 83 ASP cc_start: 0.8676 (p0) cc_final: 0.8170 (p0) REVERT: I 84 HIS cc_start: 0.8887 (m170) cc_final: 0.8471 (m170) REVERT: I 121 HIS cc_start: 0.8838 (t-170) cc_final: 0.8313 (t-170) REVERT: J 33 ASP cc_start: 0.9190 (m-30) cc_final: 0.8715 (p0) REVERT: K 2 ASN cc_start: 0.9049 (m-40) cc_final: 0.8678 (m110) REVERT: K 24 ASP cc_start: 0.8719 (t0) cc_final: 0.8229 (t0) REVERT: K 29 ASN cc_start: 0.9076 (m-40) cc_final: 0.8614 (p0) REVERT: K 31 CYS cc_start: 0.8320 (t) cc_final: 0.7841 (t) REVERT: K 53 ASP cc_start: 0.9155 (t0) cc_final: 0.8773 (t0) REVERT: L 44 MET cc_start: 0.7959 (mmt) cc_final: 0.7576 (mmt) REVERT: W 148 MET cc_start: 0.7956 (ppp) cc_final: 0.7575 (pmm) outliers start: 72 outliers final: 45 residues processed: 691 average time/residue: 0.2251 time to fit residues: 263.6753 Evaluate side-chains 668 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 616 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 316 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 304 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 360 optimal weight: 0.9990 chunk 73 optimal weight: 0.0030 chunk 90 optimal weight: 4.9990 chunk 183 optimal weight: 0.0670 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1417 HIS B 98 HIS B 111 ASN B 913 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082739 restraints weight = 70722.761| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.14 r_work: 0.2881 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 37658 Z= 0.110 Angle : 0.594 15.740 51248 Z= 0.299 Chirality : 0.043 0.186 5718 Planarity : 0.004 0.057 6309 Dihedral : 13.693 179.028 5820 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 16.17 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.13), residues: 4291 helix: 0.97 (0.14), residues: 1487 sheet: -0.09 (0.22), residues: 614 loop : -0.90 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1396 TYR 0.018 0.001 TYR H 97 PHE 0.023 0.001 PHE E 73 TRP 0.012 0.001 TRP C 49 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00248 (37625) covalent geometry : angle 0.58436 (51215) hydrogen bonds : bond 0.03179 ( 1404) hydrogen bonds : angle 4.45451 ( 3850) metal coordination : bond 0.00443 ( 33) metal coordination : angle 4.30624 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 679 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7989 (pm20) cc_final: 0.7594 (pm20) REVERT: A 62 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9165 (mm-40) REVERT: A 109 CYS cc_start: 0.9545 (t) cc_final: 0.9247 (t) REVERT: A 274 ASP cc_start: 0.8516 (t70) cc_final: 0.8198 (t70) REVERT: A 317 MET cc_start: 0.9026 (tmm) cc_final: 0.8344 (tmm) REVERT: A 337 LYS cc_start: 0.8227 (tptp) cc_final: 0.7880 (tptp) REVERT: A 355 MET cc_start: 0.8913 (tpp) cc_final: 0.8645 (ttm) REVERT: A 370 ASP cc_start: 0.9123 (t70) cc_final: 0.8893 (t70) REVERT: A 496 PHE cc_start: 0.8514 (m-10) cc_final: 0.7751 (m-10) REVERT: A 500 GLU cc_start: 0.8280 (pt0) cc_final: 0.8073 (pt0) REVERT: A 501 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7268 (ttm) REVERT: A 634 GLU cc_start: 0.8025 (tp30) cc_final: 0.7757 (mm-30) REVERT: A 868 MET cc_start: 0.7919 (mmp) cc_final: 0.6910 (mmt) REVERT: A 872 MET cc_start: 0.8767 (ptm) cc_final: 0.8482 (ttp) REVERT: A 982 ASN cc_start: 0.8414 (t0) cc_final: 0.8083 (t0) REVERT: A 1192 TRP cc_start: 0.8709 (p90) cc_final: 0.8062 (p90) REVERT: A 1284 PHE cc_start: 0.7835 (t80) cc_final: 0.7544 (t80) REVERT: A 1293 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9196 (mm) REVERT: A 1298 LEU cc_start: 0.9370 (mp) cc_final: 0.9135 (mp) REVERT: A 1353 ASP cc_start: 0.9090 (t0) cc_final: 0.8579 (t0) REVERT: A 1428 MET cc_start: 0.9134 (tmm) cc_final: 0.8836 (tmm) REVERT: A 1434 GLU cc_start: 0.8985 (pt0) cc_final: 0.8643 (pt0) REVERT: B 53 MET cc_start: 0.8937 (mmp) cc_final: 0.8683 (mmm) REVERT: B 108 MET cc_start: 0.9203 (ttm) cc_final: 0.8931 (ttp) REVERT: B 347 MET cc_start: 0.7040 (tpp) cc_final: 0.6351 (tpp) REVERT: B 422 PHE cc_start: 0.8238 (t80) cc_final: 0.7883 (t80) REVERT: B 508 MET cc_start: 0.9199 (mmp) cc_final: 0.7855 (mmp) REVERT: B 563 ASP cc_start: 0.8800 (t70) cc_final: 0.8515 (t0) REVERT: B 579 ASP cc_start: 0.8310 (t0) cc_final: 0.7795 (t0) REVERT: B 671 GLU cc_start: 0.9156 (tp30) cc_final: 0.8952 (tp30) REVERT: B 789 ASN cc_start: 0.8513 (p0) cc_final: 0.7696 (p0) REVERT: B 840 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.2627 (ttm) REVERT: B 854 ILE cc_start: 0.9333 (tp) cc_final: 0.8950 (tp) REVERT: B 910 THR cc_start: 0.9285 (t) cc_final: 0.8850 (m) REVERT: B 1048 TYR cc_start: 0.9087 (m-80) cc_final: 0.8686 (m-80) REVERT: C 83 GLN cc_start: 0.9258 (mt0) cc_final: 0.8953 (mt0) REVERT: C 186 TYR cc_start: 0.9263 (p90) cc_final: 0.9032 (p90) REVERT: C 265 HIS cc_start: 0.8741 (t-90) cc_final: 0.8469 (t-90) REVERT: E 79 GLU cc_start: 0.8955 (mp0) cc_final: 0.8376 (pm20) REVERT: E 92 GLN cc_start: 0.8548 (mm110) cc_final: 0.8281 (mm-40) REVERT: E 94 MET cc_start: 0.9442 (mmp) cc_final: 0.8916 (mmm) REVERT: E 108 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8825 (tm-30) REVERT: E 120 ASP cc_start: 0.7661 (p0) cc_final: 0.7450 (p0) REVERT: E 138 ASN cc_start: 0.8261 (t0) cc_final: 0.7850 (t0) REVERT: F 61 GLU cc_start: 0.9208 (pm20) cc_final: 0.8989 (pm20) REVERT: F 115 TYR cc_start: 0.8956 (p90) cc_final: 0.8431 (p90) REVERT: G 60 GLN cc_start: 0.8625 (mm110) cc_final: 0.8157 (mt0) REVERT: H 8 ASP cc_start: 0.7531 (t0) cc_final: 0.7265 (t0) REVERT: H 31 GLU cc_start: 0.8111 (pm20) cc_final: 0.7888 (pm20) REVERT: H 74 GLU cc_start: 0.8558 (mp0) cc_final: 0.8339 (mp0) REVERT: H 75 TYR cc_start: 0.9293 (t80) cc_final: 0.8980 (t80) REVERT: H 89 GLU cc_start: 0.8197 (pp20) cc_final: 0.7746 (pp20) REVERT: H 100 GLU cc_start: 0.8361 (pp20) cc_final: 0.8156 (pp20) REVERT: H 126 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7089 (mp-120) REVERT: I 23 MET cc_start: 0.8056 (tpp) cc_final: 0.7815 (tpp) REVERT: I 47 GLU cc_start: 0.8954 (pp20) cc_final: 0.8619 (pp20) REVERT: I 83 ASP cc_start: 0.8725 (p0) cc_final: 0.8240 (p0) REVERT: I 84 HIS cc_start: 0.8908 (m170) cc_final: 0.8528 (m170) REVERT: I 121 HIS cc_start: 0.8876 (t-170) cc_final: 0.8393 (t-170) REVERT: J 33 ASP cc_start: 0.9228 (m-30) cc_final: 0.8664 (p0) REVERT: K 2 ASN cc_start: 0.9042 (m-40) cc_final: 0.8644 (m110) REVERT: K 16 GLU cc_start: 0.6265 (pm20) cc_final: 0.5790 (pm20) REVERT: K 24 ASP cc_start: 0.8745 (t0) cc_final: 0.8152 (t0) REVERT: K 29 ASN cc_start: 0.9083 (m-40) cc_final: 0.8705 (p0) REVERT: K 31 CYS cc_start: 0.8267 (t) cc_final: 0.7801 (t) REVERT: K 38 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8709 (mm-30) REVERT: L 44 MET cc_start: 0.7987 (mmt) cc_final: 0.7488 (mmm) REVERT: W 148 MET cc_start: 0.7904 (ppp) cc_final: 0.7493 (pmm) outliers start: 69 outliers final: 35 residues processed: 706 average time/residue: 0.2267 time to fit residues: 271.9046 Evaluate side-chains 662 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 623 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 225 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 431 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 181 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN A 885 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN I 74 GLN I 100 HIS Q 44 GLN R 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075266 restraints weight = 71479.156| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.01 r_work: 0.2712 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 37658 Z= 0.264 Angle : 0.688 15.249 51248 Z= 0.349 Chirality : 0.045 0.187 5718 Planarity : 0.005 0.071 6309 Dihedral : 13.712 179.686 5820 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.65 % Allowed : 16.46 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.13), residues: 4291 helix: 0.95 (0.14), residues: 1496 sheet: -0.20 (0.21), residues: 635 loop : -0.80 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 69 TYR 0.025 0.002 TYR B 766 PHE 0.029 0.002 PHE L 55 TRP 0.016 0.002 TRP A1210 HIS 0.010 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00606 (37625) covalent geometry : angle 0.68021 (51215) hydrogen bonds : bond 0.03779 ( 1404) hydrogen bonds : angle 4.51729 ( 3850) metal coordination : bond 0.00948 ( 33) metal coordination : angle 4.13116 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 614 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8076 (pm20) cc_final: 0.7610 (pm20) REVERT: A 109 CYS cc_start: 0.9604 (t) cc_final: 0.9287 (t) REVERT: A 220 ARG cc_start: 0.9273 (ttm-80) cc_final: 0.8968 (tpp80) REVERT: A 253 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 274 ASP cc_start: 0.8698 (t70) cc_final: 0.8400 (t70) REVERT: A 341 GLN cc_start: 0.9173 (mm110) cc_final: 0.8910 (mm-40) REVERT: A 347 GLU cc_start: 0.8738 (tp30) cc_final: 0.8021 (tm-30) REVERT: A 496 PHE cc_start: 0.9139 (m-10) cc_final: 0.8643 (m-10) REVERT: A 552 ASP cc_start: 0.8723 (p0) cc_final: 0.8516 (p0) REVERT: A 634 GLU cc_start: 0.8224 (tp30) cc_final: 0.7956 (mm-30) REVERT: A 683 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 794 GLU cc_start: 0.8963 (pt0) cc_final: 0.8282 (pp20) REVERT: A 872 MET cc_start: 0.8563 (ptm) cc_final: 0.8266 (ttp) REVERT: A 962 ASP cc_start: 0.9469 (t70) cc_final: 0.9262 (t70) REVERT: A 974 ASP cc_start: 0.8162 (t0) cc_final: 0.7917 (t0) REVERT: A 982 ASN cc_start: 0.8686 (t0) cc_final: 0.8263 (t0) REVERT: A 1146 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8183 (tp-100) REVERT: A 1192 TRP cc_start: 0.8817 (p90) cc_final: 0.8180 (p90) REVERT: A 1262 MET cc_start: 0.8150 (ppp) cc_final: 0.7764 (ppp) REVERT: A 1284 PHE cc_start: 0.8200 (t80) cc_final: 0.7888 (t80) REVERT: A 1293 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9214 (mm) REVERT: A 1298 LEU cc_start: 0.9446 (mp) cc_final: 0.9219 (mp) REVERT: A 1353 ASP cc_start: 0.9189 (t0) cc_final: 0.8502 (t0) REVERT: A 1428 MET cc_start: 0.9078 (tmm) cc_final: 0.8687 (tmm) REVERT: A 1434 GLU cc_start: 0.9187 (pt0) cc_final: 0.8963 (pt0) REVERT: B 42 GLN cc_start: 0.9108 (pm20) cc_final: 0.8077 (pp30) REVERT: B 53 MET cc_start: 0.8980 (mmp) cc_final: 0.8691 (mmm) REVERT: B 108 MET cc_start: 0.9291 (ttm) cc_final: 0.8968 (ttp) REVERT: B 155 MET cc_start: 0.8942 (ptt) cc_final: 0.8506 (ptm) REVERT: B 347 MET cc_start: 0.7557 (tpp) cc_final: 0.7078 (tpp) REVERT: B 422 PHE cc_start: 0.8277 (t80) cc_final: 0.7831 (t80) REVERT: B 508 MET cc_start: 0.9428 (mmp) cc_final: 0.8033 (mmp) REVERT: B 563 ASP cc_start: 0.8863 (t70) cc_final: 0.8595 (t0) REVERT: B 579 ASP cc_start: 0.8452 (t0) cc_final: 0.7916 (t0) REVERT: B 789 ASN cc_start: 0.8663 (p0) cc_final: 0.7965 (p0) REVERT: B 840 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.3083 (ttm) REVERT: B 990 SER cc_start: 0.9620 (t) cc_final: 0.9415 (p) REVERT: C 83 GLN cc_start: 0.9348 (mt0) cc_final: 0.9037 (mt0) REVERT: C 265 HIS cc_start: 0.8807 (t-90) cc_final: 0.8547 (t-90) REVERT: E 94 MET cc_start: 0.9475 (mmp) cc_final: 0.8942 (mmm) REVERT: E 108 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8803 (tm-30) REVERT: E 120 ASP cc_start: 0.7729 (p0) cc_final: 0.7392 (p0) REVERT: E 138 ASN cc_start: 0.8368 (t0) cc_final: 0.7904 (t0) REVERT: E 203 TYR cc_start: 0.8693 (t80) cc_final: 0.8489 (t80) REVERT: F 115 TYR cc_start: 0.8980 (p90) cc_final: 0.8629 (p90) REVERT: G 60 GLN cc_start: 0.8741 (mm110) cc_final: 0.8383 (mt0) REVERT: H 8 ASP cc_start: 0.7609 (t0) cc_final: 0.7242 (t0) REVERT: H 13 LYS cc_start: 0.9106 (mttm) cc_final: 0.8839 (mmmm) REVERT: H 31 GLU cc_start: 0.8282 (pm20) cc_final: 0.7694 (pm20) REVERT: H 75 TYR cc_start: 0.9342 (t80) cc_final: 0.8980 (t80) REVERT: H 118 TYR cc_start: 0.9631 (m-80) cc_final: 0.9258 (m-80) REVERT: H 126 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7250 (mp-120) REVERT: H 145 MET cc_start: 0.7920 (mtp) cc_final: 0.7311 (mmm) REVERT: I 18 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8660 (mp10) REVERT: I 20 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8209 (p) REVERT: I 23 MET cc_start: 0.8451 (tpp) cc_final: 0.7476 (tmm) REVERT: I 45 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8191 (mm110) REVERT: I 47 GLU cc_start: 0.8965 (pp20) cc_final: 0.8681 (pp20) REVERT: I 69 ILE cc_start: 0.9417 (mm) cc_final: 0.9065 (mm) REVERT: J 33 ASP cc_start: 0.9290 (m-30) cc_final: 0.8985 (m-30) REVERT: J 54 ASP cc_start: 0.8926 (t0) cc_final: 0.8389 (t0) REVERT: J 57 GLU cc_start: 0.8990 (mp0) cc_final: 0.8520 (mp0) REVERT: K 2 ASN cc_start: 0.9092 (m-40) cc_final: 0.8776 (m110) REVERT: K 13 PHE cc_start: 0.8516 (p90) cc_final: 0.8105 (p90) REVERT: K 16 GLU cc_start: 0.6348 (pm20) cc_final: 0.5861 (pm20) REVERT: K 24 ASP cc_start: 0.8902 (t0) cc_final: 0.8217 (t0) REVERT: K 31 CYS cc_start: 0.8362 (t) cc_final: 0.7842 (t) REVERT: K 38 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8951 (mm-30) REVERT: K 53 ASP cc_start: 0.9294 (t0) cc_final: 0.8919 (t0) REVERT: L 44 MET cc_start: 0.8644 (mmt) cc_final: 0.8158 (mmt) REVERT: L 55 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7281 (t80) outliers start: 102 outliers final: 73 residues processed: 669 average time/residue: 0.2297 time to fit residues: 260.4729 Evaluate side-chains 666 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 587 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 382 optimal weight: 40.0000 chunk 7 optimal weight: 0.4980 chunk 248 optimal weight: 0.7980 chunk 323 optimal weight: 0.7980 chunk 99 optimal weight: 0.0770 chunk 383 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 378 optimal weight: 0.1980 chunk 182 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 335 optimal weight: 50.0000 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 723 ASN B 111 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 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 = 0.3897 r_free = 0.3897 target = 0.133398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079713 restraints weight = 70682.110| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.05 r_work: 0.2791 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37658 Z= 0.126 Angle : 0.623 15.734 51248 Z= 0.314 Chirality : 0.043 0.182 5718 Planarity : 0.004 0.052 6309 Dihedral : 13.677 179.347 5820 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.00 % Allowed : 18.10 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.13), residues: 4291 helix: 1.10 (0.14), residues: 1487 sheet: -0.03 (0.21), residues: 615 loop : -0.79 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 69 TYR 0.019 0.001 TYR H 97 PHE 0.032 0.001 PHE D 71 TRP 0.041 0.001 TRP A1210 HIS 0.016 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00294 (37625) covalent geometry : angle 0.61434 (51215) hydrogen bonds : bond 0.03264 ( 1404) hydrogen bonds : angle 4.38713 ( 3850) metal coordination : bond 0.00486 ( 33) metal coordination : angle 4.15586 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 652 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8067 (pm20) cc_final: 0.7651 (pm20) REVERT: A 109 CYS cc_start: 0.9556 (t) cc_final: 0.9260 (t) REVERT: A 274 ASP cc_start: 0.8561 (t70) cc_final: 0.8240 (t70) REVERT: A 337 LYS cc_start: 0.8196 (tptp) cc_final: 0.7933 (tptp) REVERT: A 341 GLN cc_start: 0.9044 (mm110) cc_final: 0.8810 (mm-40) REVERT: A 347 GLU cc_start: 0.8703 (tp30) cc_final: 0.7980 (tm-30) REVERT: A 355 MET cc_start: 0.9034 (tpp) cc_final: 0.8724 (tpp) REVERT: A 405 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8862 (tp) REVERT: A 552 ASP cc_start: 0.8583 (p0) cc_final: 0.8325 (p0) REVERT: A 634 GLU cc_start: 0.8089 (tp30) cc_final: 0.7862 (mm-30) REVERT: A 683 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 872 MET cc_start: 0.8380 (ptm) cc_final: 0.8010 (ttp) REVERT: A 962 ASP cc_start: 0.9401 (t70) cc_final: 0.9105 (t70) REVERT: A 982 ASN cc_start: 0.8620 (t0) cc_final: 0.8188 (t0) REVERT: A 983 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 1192 TRP cc_start: 0.8801 (p90) cc_final: 0.8133 (p90) REVERT: A 1262 MET cc_start: 0.8156 (ppp) cc_final: 0.7804 (ppp) REVERT: A 1284 PHE cc_start: 0.8143 (t80) cc_final: 0.7860 (t80) REVERT: A 1293 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9208 (mm) REVERT: A 1298 LEU cc_start: 0.9436 (mp) cc_final: 0.9201 (mp) REVERT: A 1353 ASP cc_start: 0.9172 (t0) cc_final: 0.8690 (t0) REVERT: A 1428 MET cc_start: 0.9060 (tmm) cc_final: 0.8773 (tmm) REVERT: A 1434 GLU cc_start: 0.9113 (pt0) cc_final: 0.8744 (pt0) REVERT: B 53 MET cc_start: 0.8917 (mmp) cc_final: 0.8639 (mmm) REVERT: B 108 MET cc_start: 0.9169 (ttm) cc_final: 0.8919 (ttp) REVERT: B 155 MET cc_start: 0.8576 (ptt) cc_final: 0.8217 (ptm) REVERT: B 266 GLU cc_start: 0.9092 (pm20) cc_final: 0.8828 (pm20) REVERT: B 347 MET cc_start: 0.7342 (tpp) cc_final: 0.7109 (tpp) REVERT: B 422 PHE cc_start: 0.8274 (t80) cc_final: 0.7810 (t80) REVERT: B 563 ASP cc_start: 0.8800 (t70) cc_final: 0.8514 (t0) REVERT: B 579 ASP cc_start: 0.8358 (t0) cc_final: 0.7819 (t0) REVERT: B 793 SER cc_start: 0.9304 (t) cc_final: 0.8829 (p) REVERT: B 806 PHE cc_start: 0.9079 (m-80) cc_final: 0.8672 (m-80) REVERT: B 840 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.3008 (ttm) REVERT: B 910 THR cc_start: 0.9421 (t) cc_final: 0.8996 (m) REVERT: B 990 SER cc_start: 0.9589 (t) cc_final: 0.9326 (p) REVERT: B 1075 MET cc_start: 0.9308 (mtp) cc_final: 0.8995 (mtp) REVERT: C 83 GLN cc_start: 0.9273 (mt0) cc_final: 0.8920 (mt0) REVERT: C 186 TYR cc_start: 0.9323 (p90) cc_final: 0.8878 (p90) REVERT: C 265 HIS cc_start: 0.8781 (t-90) cc_final: 0.8516 (t-90) REVERT: E 79 GLU cc_start: 0.8933 (mp0) cc_final: 0.8292 (pm20) REVERT: E 94 MET cc_start: 0.9445 (mmp) cc_final: 0.8940 (mmm) REVERT: E 108 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8823 (tm-30) REVERT: E 120 ASP cc_start: 0.7643 (p0) cc_final: 0.7395 (p0) REVERT: E 138 ASN cc_start: 0.8362 (t0) cc_final: 0.7885 (t0) REVERT: F 61 GLU cc_start: 0.9238 (pm20) cc_final: 0.9004 (pm20) REVERT: F 115 TYR cc_start: 0.8962 (p90) cc_final: 0.8506 (p90) REVERT: G 60 GLN cc_start: 0.8703 (mm110) cc_final: 0.8310 (mt0) REVERT: H 8 ASP cc_start: 0.7575 (t0) cc_final: 0.7272 (t0) REVERT: H 31 GLU cc_start: 0.8217 (pm20) cc_final: 0.7844 (pm20) REVERT: H 75 TYR cc_start: 0.9326 (t80) cc_final: 0.8967 (t80) REVERT: H 118 TYR cc_start: 0.9595 (m-80) cc_final: 0.9193 (m-80) REVERT: H 126 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7075 (mp-120) REVERT: I 20 CYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8545 (p) REVERT: I 23 MET cc_start: 0.8169 (tpp) cc_final: 0.7199 (tmm) REVERT: I 47 GLU cc_start: 0.9006 (pp20) cc_final: 0.8696 (pp20) REVERT: I 69 ILE cc_start: 0.9411 (mm) cc_final: 0.9070 (mm) REVERT: I 75 ASP cc_start: 0.8704 (t0) cc_final: 0.8495 (t0) REVERT: I 83 ASP cc_start: 0.8680 (p0) cc_final: 0.8272 (p0) REVERT: I 84 HIS cc_start: 0.8970 (m170) cc_final: 0.8615 (m170) REVERT: J 33 ASP cc_start: 0.9254 (m-30) cc_final: 0.8940 (m-30) REVERT: J 54 ASP cc_start: 0.8847 (t0) cc_final: 0.8303 (t0) REVERT: J 57 GLU cc_start: 0.8883 (mp0) cc_final: 0.8394 (mp0) REVERT: K 2 ASN cc_start: 0.9035 (m-40) cc_final: 0.8646 (m110) REVERT: K 13 PHE cc_start: 0.8568 (p90) cc_final: 0.8119 (p90) REVERT: K 16 GLU cc_start: 0.6475 (pm20) cc_final: 0.5948 (pm20) REVERT: K 24 ASP cc_start: 0.8876 (t0) cc_final: 0.8201 (t0) REVERT: K 31 CYS cc_start: 0.8378 (t) cc_final: 0.7843 (t) REVERT: K 38 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8924 (mm-30) REVERT: K 53 ASP cc_start: 0.9219 (t0) cc_final: 0.8787 (t0) REVERT: L 44 MET cc_start: 0.8465 (mmt) cc_final: 0.8089 (mmt) REVERT: W 148 MET cc_start: 0.7919 (ppp) cc_final: 0.7542 (pmm) outliers start: 77 outliers final: 50 residues processed: 689 average time/residue: 0.2201 time to fit residues: 257.3399 Evaluate side-chains 665 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 609 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 394 optimal weight: 10.0000 chunk 424 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 chunk 333 optimal weight: 50.0000 chunk 45 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 385 optimal weight: 10.0000 chunk 101 optimal weight: 0.0970 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079977 restraints weight = 70891.046| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.08 r_work: 0.2804 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37658 Z= 0.132 Angle : 0.629 14.904 51248 Z= 0.317 Chirality : 0.043 0.190 5718 Planarity : 0.004 0.057 6309 Dihedral : 13.654 179.849 5820 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.90 % Allowed : 18.46 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.13), residues: 4291 helix: 1.11 (0.14), residues: 1493 sheet: -0.05 (0.21), residues: 626 loop : -0.75 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1396 TYR 0.020 0.001 TYR H 97 PHE 0.042 0.001 PHE D 71 TRP 0.041 0.001 TRP A1210 HIS 0.008 0.001 HIS Q 152 Details of bonding type rmsd covalent geometry : bond 0.00307 (37625) covalent geometry : angle 0.62094 (51215) hydrogen bonds : bond 0.03210 ( 1404) hydrogen bonds : angle 4.33120 ( 3850) metal coordination : bond 0.00495 ( 33) metal coordination : angle 3.99510 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 638 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8107 (pm20) cc_final: 0.7689 (pm20) REVERT: A 109 CYS cc_start: 0.9552 (t) cc_final: 0.9233 (t) REVERT: A 274 ASP cc_start: 0.8553 (t70) cc_final: 0.8229 (t70) REVERT: A 341 GLN cc_start: 0.9070 (mm110) cc_final: 0.8840 (mm-40) REVERT: A 347 GLU cc_start: 0.8733 (tp30) cc_final: 0.8007 (tm-30) REVERT: A 405 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8766 (tp) REVERT: A 552 ASP cc_start: 0.8668 (p0) cc_final: 0.8399 (p0) REVERT: A 634 GLU cc_start: 0.8112 (tp30) cc_final: 0.7900 (mm-30) REVERT: A 683 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 872 MET cc_start: 0.8390 (ptm) cc_final: 0.8086 (ttp) REVERT: A 962 ASP cc_start: 0.9395 (t70) cc_final: 0.9060 (t70) REVERT: A 982 ASN cc_start: 0.8600 (t0) cc_final: 0.8172 (t0) REVERT: A 983 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9149 (mm) REVERT: A 1146 GLN cc_start: 0.8430 (tp-100) cc_final: 0.7911 (tp-100) REVERT: A 1192 TRP cc_start: 0.8789 (p90) cc_final: 0.8102 (p90) REVERT: A 1262 MET cc_start: 0.8168 (ppp) cc_final: 0.7837 (ppp) REVERT: A 1284 PHE cc_start: 0.8161 (t80) cc_final: 0.7878 (t80) REVERT: A 1293 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9229 (mm) REVERT: A 1298 LEU cc_start: 0.9446 (mp) cc_final: 0.9218 (mp) REVERT: A 1309 MET cc_start: 0.9381 (mtp) cc_final: 0.9177 (mtp) REVERT: A 1353 ASP cc_start: 0.9176 (t0) cc_final: 0.8580 (t0) REVERT: A 1396 ARG cc_start: 0.8499 (mtt90) cc_final: 0.8221 (mtt90) REVERT: A 1420 ASN cc_start: 0.9318 (m-40) cc_final: 0.8951 (t0) REVERT: B 53 MET cc_start: 0.8938 (mmp) cc_final: 0.8655 (mmm) REVERT: B 155 MET cc_start: 0.8534 (ptt) cc_final: 0.8187 (ptm) REVERT: B 347 MET cc_start: 0.7386 (tpp) cc_final: 0.7134 (tpp) REVERT: B 422 PHE cc_start: 0.8286 (t80) cc_final: 0.7817 (t80) REVERT: B 563 ASP cc_start: 0.8806 (t70) cc_final: 0.8519 (t0) REVERT: B 579 ASP cc_start: 0.8349 (t0) cc_final: 0.7822 (t0) REVERT: B 671 GLU cc_start: 0.9058 (tp30) cc_final: 0.8853 (tp30) REVERT: B 806 PHE cc_start: 0.9011 (m-80) cc_final: 0.8670 (m-80) REVERT: B 840 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.3118 (ttm) REVERT: B 910 THR cc_start: 0.9462 (t) cc_final: 0.9019 (m) REVERT: C 18 ASN cc_start: 0.7464 (t0) cc_final: 0.7243 (t0) REVERT: C 83 GLN cc_start: 0.9331 (mt0) cc_final: 0.9014 (mt0) REVERT: C 186 TYR cc_start: 0.9313 (p90) cc_final: 0.8829 (p90) REVERT: C 265 HIS cc_start: 0.8791 (t-90) cc_final: 0.8527 (t-90) REVERT: E 79 GLU cc_start: 0.8962 (mp0) cc_final: 0.8454 (pm20) REVERT: E 94 MET cc_start: 0.9476 (mmp) cc_final: 0.8979 (mmm) REVERT: E 108 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8828 (tm-30) REVERT: E 120 ASP cc_start: 0.7598 (p0) cc_final: 0.7347 (p0) REVERT: E 138 ASN cc_start: 0.8432 (t0) cc_final: 0.7954 (t0) REVERT: E 203 TYR cc_start: 0.8505 (t80) cc_final: 0.8303 (t80) REVERT: F 61 GLU cc_start: 0.9229 (pm20) cc_final: 0.8989 (pm20) REVERT: F 100 ARG cc_start: 0.9569 (ttm-80) cc_final: 0.9365 (ttm-80) REVERT: F 115 TYR cc_start: 0.8990 (p90) cc_final: 0.8540 (p90) REVERT: G 60 GLN cc_start: 0.8740 (mm110) cc_final: 0.8360 (mt0) REVERT: H 8 ASP cc_start: 0.7561 (t0) cc_final: 0.7225 (t0) REVERT: H 31 GLU cc_start: 0.8218 (pm20) cc_final: 0.7828 (pm20) REVERT: H 75 TYR cc_start: 0.9337 (t80) cc_final: 0.8964 (t80) REVERT: H 118 TYR cc_start: 0.9612 (m-80) cc_final: 0.9191 (m-80) REVERT: H 126 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7291 (mp-120) REVERT: I 20 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8477 (p) REVERT: I 23 MET cc_start: 0.8214 (tpp) cc_final: 0.7921 (tpp) REVERT: I 47 GLU cc_start: 0.8990 (pp20) cc_final: 0.8683 (pp20) REVERT: I 69 ILE cc_start: 0.9421 (mm) cc_final: 0.9091 (mm) REVERT: I 74 GLN cc_start: 0.8754 (tt0) cc_final: 0.8407 (tm-30) REVERT: I 83 ASP cc_start: 0.8686 (p0) cc_final: 0.8261 (p0) REVERT: I 84 HIS cc_start: 0.8984 (m170) cc_final: 0.8618 (m170) REVERT: J 33 ASP cc_start: 0.9254 (m-30) cc_final: 0.8918 (m-30) REVERT: J 54 ASP cc_start: 0.8832 (t0) cc_final: 0.8281 (t0) REVERT: J 57 GLU cc_start: 0.8899 (mp0) cc_final: 0.8383 (mp0) REVERT: K 2 ASN cc_start: 0.9023 (m-40) cc_final: 0.8629 (m110) REVERT: K 13 PHE cc_start: 0.8577 (p90) cc_final: 0.8117 (p90) REVERT: K 16 GLU cc_start: 0.6645 (pm20) cc_final: 0.6166 (pm20) REVERT: K 24 ASP cc_start: 0.8908 (t0) cc_final: 0.8227 (t0) REVERT: K 31 CYS cc_start: 0.8345 (t) cc_final: 0.7848 (t) REVERT: K 38 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8903 (mm-30) REVERT: K 53 ASP cc_start: 0.9204 (t0) cc_final: 0.8765 (t0) REVERT: L 44 MET cc_start: 0.8505 (mmt) cc_final: 0.8117 (mmt) REVERT: W 148 MET cc_start: 0.7934 (ppp) cc_final: 0.7555 (pmm) outliers start: 73 outliers final: 56 residues processed: 670 average time/residue: 0.2245 time to fit residues: 254.8926 Evaluate side-chains 679 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 617 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 270 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 286 optimal weight: 50.0000 chunk 245 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN B 111 ASN B 503 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079172 restraints weight = 70717.278| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.03 r_work: 0.2777 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37658 Z= 0.176 Angle : 0.660 15.239 51248 Z= 0.332 Chirality : 0.044 0.201 5718 Planarity : 0.004 0.052 6309 Dihedral : 13.661 179.886 5820 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.11 % Rotamer: Outliers : 2.03 % Allowed : 18.85 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.13), residues: 4291 helix: 1.09 (0.14), residues: 1498 sheet: -0.10 (0.21), residues: 648 loop : -0.73 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 40 TYR 0.025 0.001 TYR G 42 PHE 0.049 0.001 PHE D 71 TRP 0.045 0.001 TRP A1210 HIS 0.008 0.001 HIS Q 152 Details of bonding type rmsd covalent geometry : bond 0.00412 (37625) covalent geometry : angle 0.65225 (51215) hydrogen bonds : bond 0.03327 ( 1404) hydrogen bonds : angle 4.36247 ( 3850) metal coordination : bond 0.00681 ( 33) metal coordination : angle 4.00885 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 630 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8052 (pm20) cc_final: 0.7623 (pm20) REVERT: A 109 CYS cc_start: 0.9521 (t) cc_final: 0.9215 (t) REVERT: A 274 ASP cc_start: 0.8501 (t70) cc_final: 0.8188 (t70) REVERT: A 341 GLN cc_start: 0.9077 (mm110) cc_final: 0.8661 (mm-40) REVERT: A 347 GLU cc_start: 0.8750 (tp30) cc_final: 0.8075 (tm-30) REVERT: A 496 PHE cc_start: 0.8792 (m-10) cc_final: 0.8494 (m-10) REVERT: A 634 GLU cc_start: 0.8014 (tp30) cc_final: 0.7778 (mm-30) REVERT: A 683 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 861 GLN cc_start: 0.9083 (mm110) cc_final: 0.8861 (mm110) REVERT: A 872 MET cc_start: 0.8440 (ptm) cc_final: 0.8121 (ttp) REVERT: A 982 ASN cc_start: 0.8546 (t0) cc_final: 0.8127 (t0) REVERT: A 983 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9077 (mm) REVERT: A 1146 GLN cc_start: 0.8411 (tp-100) cc_final: 0.7911 (tp-100) REVERT: A 1192 TRP cc_start: 0.8857 (p90) cc_final: 0.8264 (p90) REVERT: A 1262 MET cc_start: 0.8209 (ppp) cc_final: 0.7872 (ppp) REVERT: A 1284 PHE cc_start: 0.8160 (t80) cc_final: 0.7894 (t80) REVERT: A 1293 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9252 (mm) REVERT: A 1298 LEU cc_start: 0.9466 (mp) cc_final: 0.9265 (mp) REVERT: A 1353 ASP cc_start: 0.9166 (t0) cc_final: 0.8559 (t0) REVERT: A 1420 ASN cc_start: 0.9306 (m-40) cc_final: 0.8958 (t0) REVERT: B 53 MET cc_start: 0.8826 (mmp) cc_final: 0.8544 (mmm) REVERT: B 155 MET cc_start: 0.8667 (ptt) cc_final: 0.8234 (ptm) REVERT: B 347 MET cc_start: 0.7300 (tpp) cc_final: 0.6886 (tpp) REVERT: B 422 PHE cc_start: 0.8257 (t80) cc_final: 0.7786 (t80) REVERT: B 563 ASP cc_start: 0.8814 (t70) cc_final: 0.8529 (t0) REVERT: B 579 ASP cc_start: 0.8394 (t0) cc_final: 0.7851 (t0) REVERT: B 728 MET cc_start: 0.8844 (mtm) cc_final: 0.8619 (mtm) REVERT: B 793 SER cc_start: 0.9316 (t) cc_final: 0.8814 (p) REVERT: B 806 PHE cc_start: 0.9191 (m-80) cc_final: 0.8797 (m-80) REVERT: B 840 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.3438 (ttm) REVERT: C 18 ASN cc_start: 0.7258 (t0) cc_final: 0.7053 (t0) REVERT: C 83 GLN cc_start: 0.9320 (mt0) cc_final: 0.8980 (mt0) REVERT: C 265 HIS cc_start: 0.8773 (t-90) cc_final: 0.8520 (t-90) REVERT: E 21 CYS cc_start: 0.9620 (m) cc_final: 0.9347 (m) REVERT: E 50 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8962 (mp0) REVERT: E 94 MET cc_start: 0.9476 (mmp) cc_final: 0.8975 (mmm) REVERT: E 108 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8850 (tm-30) REVERT: E 118 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9048 (mm) REVERT: E 120 ASP cc_start: 0.7641 (p0) cc_final: 0.7365 (p0) REVERT: E 138 ASN cc_start: 0.8356 (t0) cc_final: 0.7858 (t0) REVERT: E 203 TYR cc_start: 0.8516 (t80) cc_final: 0.8312 (t80) REVERT: F 61 GLU cc_start: 0.9224 (pm20) cc_final: 0.8958 (pm20) REVERT: F 84 GLU cc_start: 0.9213 (mp0) cc_final: 0.8530 (mp0) REVERT: F 100 ARG cc_start: 0.9535 (ttm-80) cc_final: 0.9334 (ttm-80) REVERT: F 115 TYR cc_start: 0.8982 (p90) cc_final: 0.8547 (p90) REVERT: G 60 GLN cc_start: 0.8685 (mm110) cc_final: 0.8317 (mt0) REVERT: H 8 ASP cc_start: 0.7535 (t0) cc_final: 0.7163 (t0) REVERT: H 31 GLU cc_start: 0.8193 (pm20) cc_final: 0.7813 (pm20) REVERT: H 75 TYR cc_start: 0.9341 (t80) cc_final: 0.8986 (t80) REVERT: H 126 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7073 (mp-120) REVERT: I 23 MET cc_start: 0.8325 (tpp) cc_final: 0.8015 (tpp) REVERT: I 47 GLU cc_start: 0.9003 (pp20) cc_final: 0.8695 (pp20) REVERT: I 69 ILE cc_start: 0.9400 (mm) cc_final: 0.9055 (mm) REVERT: J 33 ASP cc_start: 0.9268 (m-30) cc_final: 0.8912 (m-30) REVERT: J 57 GLU cc_start: 0.8884 (mp0) cc_final: 0.8582 (mm-30) REVERT: K 2 ASN cc_start: 0.9025 (m-40) cc_final: 0.8640 (m110) REVERT: K 13 PHE cc_start: 0.8551 (p90) cc_final: 0.8100 (p90) REVERT: K 16 GLU cc_start: 0.6587 (pm20) cc_final: 0.6146 (pm20) REVERT: K 24 ASP cc_start: 0.8885 (t0) cc_final: 0.8156 (t0) REVERT: K 31 CYS cc_start: 0.8365 (t) cc_final: 0.7833 (t) REVERT: K 53 ASP cc_start: 0.9198 (t0) cc_final: 0.8752 (t0) REVERT: L 16 ILE cc_start: 0.8915 (pt) cc_final: 0.8629 (tp) REVERT: L 44 MET cc_start: 0.8571 (mmt) cc_final: 0.8096 (mmt) REVERT: W 148 MET cc_start: 0.7941 (ppp) cc_final: 0.7559 (pmm) outliers start: 78 outliers final: 60 residues processed: 669 average time/residue: 0.2286 time to fit residues: 258.8975 Evaluate side-chains 663 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 598 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 1 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 389 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN B 111 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.133331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079564 restraints weight = 70587.837| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.06 r_work: 0.2784 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37658 Z= 0.153 Angle : 0.681 24.191 51248 Z= 0.336 Chirality : 0.044 0.210 5718 Planarity : 0.004 0.058 6309 Dihedral : 13.681 179.848 5820 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.11 % Rotamer: Outliers : 1.82 % Allowed : 19.47 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.13), residues: 4291 helix: 1.08 (0.14), residues: 1496 sheet: -0.12 (0.21), residues: 649 loop : -0.72 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 40 TYR 0.022 0.001 TYR H 97 PHE 0.043 0.001 PHE L 55 TRP 0.053 0.001 TRP A1210 HIS 0.007 0.001 HIS Q 152 Details of bonding type rmsd covalent geometry : bond 0.00361 (37625) covalent geometry : angle 0.66227 (51215) hydrogen bonds : bond 0.03240 ( 1404) hydrogen bonds : angle 4.36773 ( 3850) metal coordination : bond 0.00850 ( 33) metal coordination : angle 6.22674 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 625 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8086 (pm20) cc_final: 0.7669 (pm20) REVERT: A 109 CYS cc_start: 0.9532 (t) cc_final: 0.9190 (t) REVERT: A 274 ASP cc_start: 0.8440 (t70) cc_final: 0.8110 (t70) REVERT: A 337 LYS cc_start: 0.8288 (tptp) cc_final: 0.8073 (tppt) REVERT: A 347 GLU cc_start: 0.8741 (tp30) cc_final: 0.8073 (tm-30) REVERT: A 634 GLU cc_start: 0.8007 (tp30) cc_final: 0.7783 (mm-30) REVERT: A 683 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 872 MET cc_start: 0.8380 (ptm) cc_final: 0.7951 (ttp) REVERT: A 962 ASP cc_start: 0.9452 (t0) cc_final: 0.9174 (t70) REVERT: A 982 ASN cc_start: 0.8548 (t0) cc_final: 0.8128 (t0) REVERT: A 983 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 1146 GLN cc_start: 0.8413 (tp-100) cc_final: 0.7890 (tp-100) REVERT: A 1192 TRP cc_start: 0.8860 (p90) cc_final: 0.8283 (p90) REVERT: A 1262 MET cc_start: 0.8191 (ppp) cc_final: 0.7853 (ppp) REVERT: A 1284 PHE cc_start: 0.8182 (t80) cc_final: 0.7940 (t80) REVERT: A 1293 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9245 (mm) REVERT: A 1298 LEU cc_start: 0.9457 (mp) cc_final: 0.9238 (mp) REVERT: A 1353 ASP cc_start: 0.9162 (t0) cc_final: 0.8563 (t0) REVERT: A 1361 ASP cc_start: 0.8467 (t0) cc_final: 0.8086 (p0) REVERT: A 1396 ARG cc_start: 0.8475 (mtt90) cc_final: 0.8240 (mtt90) REVERT: A 1420 ASN cc_start: 0.9302 (m-40) cc_final: 0.8955 (t0) REVERT: B 53 MET cc_start: 0.8837 (mmp) cc_final: 0.8555 (mmm) REVERT: B 155 MET cc_start: 0.8627 (ptt) cc_final: 0.8219 (ptm) REVERT: B 347 MET cc_start: 0.7388 (tpp) cc_final: 0.7026 (tpp) REVERT: B 407 MET cc_start: 0.8989 (mtm) cc_final: 0.8773 (mtt) REVERT: B 422 PHE cc_start: 0.8274 (t80) cc_final: 0.7790 (t80) REVERT: B 563 ASP cc_start: 0.8780 (t70) cc_final: 0.8490 (t0) REVERT: B 579 ASP cc_start: 0.8326 (t0) cc_final: 0.7767 (t0) REVERT: B 728 MET cc_start: 0.9046 (mtm) cc_final: 0.8842 (mtm) REVERT: B 806 PHE cc_start: 0.9124 (m-80) cc_final: 0.8724 (m-80) REVERT: B 840 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.3706 (ttm) REVERT: C 83 GLN cc_start: 0.9328 (mt0) cc_final: 0.8992 (mt0) REVERT: C 265 HIS cc_start: 0.8815 (t-90) cc_final: 0.8566 (t-90) REVERT: E 21 CYS cc_start: 0.9626 (m) cc_final: 0.9213 (m) REVERT: E 94 MET cc_start: 0.9461 (mmp) cc_final: 0.8979 (mmm) REVERT: E 110 MET cc_start: 0.7961 (mtm) cc_final: 0.7534 (mtm) REVERT: E 120 ASP cc_start: 0.7617 (p0) cc_final: 0.7359 (p0) REVERT: E 138 ASN cc_start: 0.8329 (t0) cc_final: 0.7817 (t0) REVERT: E 203 TYR cc_start: 0.8492 (t80) cc_final: 0.8284 (t80) REVERT: F 50 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8508 (tmmt) REVERT: F 61 GLU cc_start: 0.9239 (pm20) cc_final: 0.8954 (pm20) REVERT: F 115 TYR cc_start: 0.8986 (p90) cc_final: 0.8569 (p90) REVERT: G 60 GLN cc_start: 0.8689 (mm110) cc_final: 0.8311 (mt0) REVERT: H 8 ASP cc_start: 0.7551 (t0) cc_final: 0.7164 (t0) REVERT: H 31 GLU cc_start: 0.8222 (pm20) cc_final: 0.7855 (pm20) REVERT: H 75 TYR cc_start: 0.9330 (t80) cc_final: 0.8979 (t80) REVERT: H 118 TYR cc_start: 0.9530 (m-80) cc_final: 0.9255 (m-80) REVERT: H 123 MET cc_start: 0.8972 (ptm) cc_final: 0.8746 (ptm) REVERT: H 126 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7152 (mp-120) REVERT: I 47 GLU cc_start: 0.9014 (pp20) cc_final: 0.8695 (pp20) REVERT: I 69 ILE cc_start: 0.9390 (mm) cc_final: 0.9047 (mm) REVERT: I 74 GLN cc_start: 0.8729 (tt0) cc_final: 0.8247 (tm-30) REVERT: I 84 HIS cc_start: 0.8915 (m170) cc_final: 0.8596 (m170) REVERT: J 33 ASP cc_start: 0.9275 (m-30) cc_final: 0.8919 (m-30) REVERT: J 54 ASP cc_start: 0.8712 (t0) cc_final: 0.8123 (t0) REVERT: J 57 GLU cc_start: 0.8882 (mp0) cc_final: 0.8409 (mp0) REVERT: K 2 ASN cc_start: 0.8970 (m-40) cc_final: 0.8586 (m110) REVERT: K 13 PHE cc_start: 0.8560 (p90) cc_final: 0.8039 (p90) REVERT: K 16 GLU cc_start: 0.6548 (pm20) cc_final: 0.6055 (pm20) REVERT: K 24 ASP cc_start: 0.8916 (t0) cc_final: 0.8180 (t0) REVERT: K 31 CYS cc_start: 0.8433 (t) cc_final: 0.7888 (t) REVERT: K 53 ASP cc_start: 0.9200 (t0) cc_final: 0.8750 (t0) REVERT: L 44 MET cc_start: 0.8666 (mmt) cc_final: 0.8037 (mmm) REVERT: W 148 MET cc_start: 0.7893 (ppp) cc_final: 0.7517 (pmm) outliers start: 70 outliers final: 59 residues processed: 660 average time/residue: 0.2262 time to fit residues: 252.6726 Evaluate side-chains 675 residues out of total 3847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 612 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain Q residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 280 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 324 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 399 optimal weight: 30.0000 chunk 316 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 238 optimal weight: 0.0060 overall best weight: 0.7776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080126 restraints weight = 70160.842| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.04 r_work: 0.2796 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.003 0.078 37658 Z= 0.147 Angle : 0.676 23.427 51248 Z= 0.333 Chirality : 0.044 0.205 5718 Planarity : 0.004 0.052 6309 Dihedral : 13.687 179.964 5820 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 1.79 % Allowed : 19.81 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.13), residues: 4291 helix: 1.08 (0.14), residues: 1496 sheet: -0.09 (0.21), residues: 649 loop : -0.74 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1396 TYR 0.021 0.001 TYR H 97 PHE 0.035 0.001 PHE L 55 TRP 0.062 0.001 TRP A1210 HIS 0.006 0.001 HIS Q 152 Details of bonding type rmsd covalent geometry : bond 0.00347 (37625) covalent geometry : angle 0.65974 (51215) hydrogen bonds : bond 0.03200 ( 1404) hydrogen bonds : angle 4.36849 ( 3850) metal coordination : bond 0.00752 ( 33) metal coordination : angle 5.77479 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11803.71 seconds wall clock time: 203 minutes 5.92 seconds (12185.92 seconds total)