Starting phenix.real_space_refine on Sun Jul 5 23:38:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851.map" model { file = "/net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ap9_11851/07_2026/7ap9_11851_neut.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 4 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 19801 2.51 5 N 5138 2.21 5 O 5784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30881 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10188 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9091 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2484 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1192 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3903 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 443} Chain breaks: 3 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "S" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 952 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 89.098 103.263 61.297 1.00133.50 S ATOM 382 SG CYS A 52 92.766 103.153 60.361 1.00126.58 S ATOM 434 SG CYS A 59 91.093 100.167 62.119 1.00122.37 S ATOM 694 SG CYS A 90 75.503 100.632 108.162 1.00155.92 S ATOM 718 SG CYS A 93 77.134 103.838 109.373 1.00162.06 S ATOM 1016 SG CYS A 130 76.679 101.014 111.747 1.00161.58 S ATOM 1059 SG CYS A 135 73.631 102.857 110.714 1.00165.37 S ATOM 18688 SG CYS B1087 99.216 104.479 75.606 1.00109.10 S ATOM 18711 SG CYS B1090 95.658 103.225 76.196 1.00111.20 S ATOM 18800 SG CYS B1103 96.127 105.787 73.776 1.00111.30 S ATOM 18825 SG CYS B1106 96.658 106.724 77.394 1.00115.40 S ATOM 27059 SG CYS I 326 101.651 96.021 37.377 1.00214.92 S ATOM 27372 SG CYS I 363 99.819 92.714 38.389 1.00191.93 S ATOM 27396 SG CYS I 366 103.225 93.533 39.896 1.00189.01 S Time building chain proxies: 6.35, per 1000 atoms: 0.21 Number of scatterers: 30881 At special positions: 0 Unit cell: (162.716, 152.081, 153.144, 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 4 29.99 S 142 16.00 P 11 15.00 Mg 1 11.99 O 5784 8.00 N 5138 7.00 C 19801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS J 39 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 328 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 366 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 363 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 326 " Number of angles added : 18 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 48 sheets defined 42.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.604A pdb=" N LYS A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.637A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 6.156A pdb=" N LYS A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.726A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.753A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 488 removed outlier: 4.245A pdb=" N ARG A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.552A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.917A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 573 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.719A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 Processing helix chain 'A' and resid 622 through 656 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 809 through 821 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.720A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.605A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.704A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 944 through 946 No H-bonds generated for 'chain 'A' and resid 944 through 946' Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.193A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.526A pdb=" N VAL A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.375A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1170 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 3.603A pdb=" N TYR A1252 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.650A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.512A pdb=" N ASN B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.846A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.621A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.523A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.606A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 391 removed outlier: 3.636A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 558 removed outlier: 3.570A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.079A pdb=" N SER B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.580A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.636A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.792A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.617A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.834A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.689A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 924 removed outlier: 4.389A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.138A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.516A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 1021 through 1026 removed outlier: 3.620A pdb=" N LYS B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.659A pdb=" N TYR B1081 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1134 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 4.082A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.313A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.735A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 157' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.914A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.520A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.521A pdb=" N ARG C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.736A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.581A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 4.043A pdb=" N TYR E 101 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 101' Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.792A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 143 through 161 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 186 removed outlier: 5.940A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.704A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 326 through 336 removed outlier: 3.883A pdb=" N ILE I 330 " --> pdb=" O CYS I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 688 through 694 removed outlier: 4.141A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.523A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.490A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.602A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.560A pdb=" N VAL J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 59 through 63 Processing helix chain 'S' and resid 72 through 81 Processing helix chain 'S' and resid 82 through 85 Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 131 removed outlier: 3.572A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.385A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.222A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.863A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.441A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.505A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.516A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB2, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB3, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB4, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB5, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.837A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.837A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.653A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE B 98 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU B 121 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 100 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER B 119 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 102 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.653A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B 99 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.984A pdb=" N VAL B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.712A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.441A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC7, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.811A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.835A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.835A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 857 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD2, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.497A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 996 through 997 removed outlier: 3.683A pdb=" N LYS B1002 " --> pdb=" O ASP B 997 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.552A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AE1, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.461A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.221A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 90 removed outlier: 4.420A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE7, first strand: chain 'I' and resid 121 through 124 removed outlier: 4.315A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.384A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AF1, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AF2, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AF3, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.192A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9820 1.34 - 1.46: 7445 1.46 - 1.59: 14021 1.59 - 1.71: 20 1.71 - 1.83: 223 Bond restraints: 31529 Sorted by residual: bond pdb=" C ARG B 347 " pdb=" N TYR B 348 " ideal model delta sigma weight residual 1.331 1.234 0.097 3.12e-02 1.03e+03 9.71e+00 bond pdb=" C1' DT T 20 " pdb=" N1 DT T 20 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" C ILE B 909 " pdb=" N THR B 910 " ideal model delta sigma weight residual 1.331 1.272 0.059 2.07e-02 2.33e+03 8.25e+00 bond pdb=" C1' DT T 21 " pdb=" N1 DT T 21 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.72e+00 bond pdb=" C3' DA T 24 " pdb=" C2' DA T 24 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.08e+00 ... (remaining 31524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 41355 1.63 - 3.25: 1095 3.25 - 4.88: 167 4.88 - 6.51: 44 6.51 - 8.14: 1 Bond angle restraints: 42662 Sorted by residual: angle pdb=" N VAL B 401 " pdb=" CA VAL B 401 " pdb=" C VAL B 401 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" N3 DT T 20 " pdb=" C4 DT T 20 " pdb=" O4 DT T 20 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT T 23 " pdb=" C4 DT T 23 " pdb=" O4 DT T 23 " ideal model delta sigma weight residual 119.90 122.25 -2.35 6.00e-01 2.78e+00 1.54e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.14 -2.24 6.00e-01 2.78e+00 1.40e+01 angle pdb=" O4 DT T 21 " pdb=" C4 DT T 21 " pdb=" C5 DT T 21 " ideal model delta sigma weight residual 124.90 122.45 2.45 7.00e-01 2.04e+00 1.22e+01 ... (remaining 42657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 17806 17.26 - 34.51: 1053 34.51 - 51.77: 214 51.77 - 69.03: 51 69.03 - 86.28: 11 Dihedral angle restraints: 19135 sinusoidal: 7941 harmonic: 11194 Sorted by residual: dihedral pdb=" CB CYS J 7 " pdb=" SG CYS J 7 " pdb=" SG CYS J 39 " pdb=" CB CYS J 39 " ideal model delta sinusoidal sigma weight residual -86.00 -162.14 76.14 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA VAL I 660 " pdb=" C VAL I 660 " pdb=" N HIS I 661 " pdb=" CA HIS I 661 " ideal model delta harmonic sigma weight residual -180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 19132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2758 0.035 - 0.071: 1460 0.071 - 0.106: 409 0.106 - 0.141: 189 0.141 - 0.176: 13 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CA PHE A 938 " pdb=" N PHE A 938 " pdb=" C PHE A 938 " pdb=" CB PHE A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" C3' DT T 21 " pdb=" C4' DT T 21 " pdb=" O3' DT T 21 " pdb=" C2' DT T 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" C3' DA T 22 " pdb=" C4' DA T 22 " pdb=" O3' DA T 22 " pdb=" C2' DA T 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 4826 not shown) Planarity restraints: 5361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 856 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ARG B 856 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG B 856 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 857 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.020 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE A 938 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 35 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C TYR B 35 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR B 35 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 36 " 0.012 2.00e-02 2.50e+03 ... (remaining 5358 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 395 2.60 - 3.17: 28526 3.17 - 3.75: 46198 3.75 - 4.32: 69204 4.32 - 4.90: 114528 Nonbonded interactions: 258851 Sorted by model distance: nonbonded pdb=" OG1 THR B 303 " pdb=" O ASN B 305 " model vdw 2.023 3.040 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.028 3.040 nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.041 2.170 nonbonded pdb=" OH TYR B 512 " pdb=" OD2 ASP B 551 " model vdw 2.064 3.040 nonbonded pdb=" O LYS B 60 " pdb=" OG1 THR B 63 " model vdw 2.079 3.040 ... (remaining 258846 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.008 0.097 31546 Z= 0.387 Angle : 0.681 8.678 42682 Z= 0.386 Chirality : 0.047 0.176 4829 Planarity : 0.004 0.039 5361 Dihedral : 12.024 86.284 11904 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.91 % Allowed : 5.31 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3752 helix: 0.91 (0.14), residues: 1356 sheet: -1.09 (0.21), residues: 561 loop : -0.92 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 317 TYR 0.023 0.002 TYR S 134 PHE 0.039 0.002 PHE A 938 TRP 0.014 0.001 TRP A1054 HIS 0.006 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.39 (31529) covalent geometry : angle 0.67832 / 0.39 (42662) SS BOND : bond 0.00878 / 0.46 ( 1) SS BOND : angle 2.34498 / 1.56 ( 2) hydrogen bonds : bond 0.13140 / 8.80 ( 1287) hydrogen bonds : angle 6.46530 / 4.51 ( 3651) metal coordination : bond 0.01404 / 0.81 ( 16) metal coordination : angle 2.96795 / 2.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 322 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9077 (mmmt) REVERT: A 124 LEU cc_start: 0.8971 (mt) cc_final: 0.8693 (pp) REVERT: A 219 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8692 (tp30) REVERT: A 226 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8689 (mmp) REVERT: A 591 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9049 (tt) REVERT: A 791 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9263 (tt) REVERT: A 1062 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6991 (t0) REVERT: B 65 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8013 (ptm-80) REVERT: B 67 MET cc_start: 0.8558 (mmm) cc_final: 0.7268 (mmm) REVERT: B 184 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8617 (ttpp) REVERT: B 372 ASP cc_start: 0.8796 (m-30) cc_final: 0.8582 (t0) REVERT: B 478 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7857 (ttp80) REVERT: B 786 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8844 (m-40) REVERT: B 868 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8105 (mtp85) REVERT: B 1043 GLU cc_start: 0.8210 (tt0) cc_final: 0.7930 (tt0) REVERT: E 98 ASN cc_start: 0.8983 (t0) cc_final: 0.8774 (t0) REVERT: E 144 GLU cc_start: 0.8623 (tt0) cc_final: 0.8128 (pt0) REVERT: G 20 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9090 (p) REVERT: G 124 PHE cc_start: 0.7815 (m-80) cc_final: 0.7608 (m-80) REVERT: G 142 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8302 (ttt) REVERT: I 176 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: I 181 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8465 (mp10) REVERT: I 317 ARG cc_start: 0.5583 (OUTLIER) cc_final: 0.4174 (ttp80) REVERT: I 342 TYR cc_start: 0.6866 (t80) cc_final: 0.6620 (t80) REVERT: I 776 GLN cc_start: 0.9293 (tt0) cc_final: 0.9065 (tt0) REVERT: J 21 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8878 (pp) REVERT: S 49 SER cc_start: 0.9484 (t) cc_final: 0.9209 (p) REVERT: S 59 THR cc_start: 0.8762 (p) cc_final: 0.8369 (t) REVERT: S 64 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: S 116 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9044 (mm-30) REVERT: S 133 GLU cc_start: 0.8505 (tp30) cc_final: 0.8102 (tp30) outliers start: 101 outliers final: 31 residues processed: 411 average time/residue: 0.2194 time to fit residues: 137.9037 Evaluate side-chains 248 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 317 ARG Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 738 ARG Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 64 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 947 HIS A1073 ASN B 754 GLN B1020 HIS F 111 GLN G 37 HIS I 735 ASN S 90 ASN ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.042305 restraints weight = 98842.024| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.10 r_work: 0.2521 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31546 Z= 0.145 Angle : 0.598 11.887 42682 Z= 0.320 Chirality : 0.045 0.268 4829 Planarity : 0.004 0.049 5361 Dihedral : 7.546 58.853 4356 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.05 % Allowed : 8.25 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3752 helix: 1.23 (0.14), residues: 1367 sheet: -0.72 (0.22), residues: 565 loop : -0.78 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 90 TYR 0.020 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.015 0.001 TRP A 365 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (31529) covalent geometry : angle 0.59473 / 0.32 (42662) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 2.79404 / 1.86 ( 2) hydrogen bonds : bond 0.04765 / 3.25 ( 1287) hydrogen bonds : angle 5.22540 / 3.64 ( 3651) metal coordination : bond 0.00905 / 0.71 ( 16) metal coordination : angle 2.72990 / 1.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8859 (p0) cc_final: 0.8607 (p0) REVERT: A 122 LYS cc_start: 0.9290 (mtmt) cc_final: 0.8999 (mmmt) REVERT: A 124 LEU cc_start: 0.8895 (mt) cc_final: 0.8608 (pp) REVERT: A 219 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8758 (tp30) REVERT: A 226 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8977 (mmp) REVERT: A 791 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9258 (tt) REVERT: B 67 MET cc_start: 0.8649 (mmm) cc_final: 0.7938 (mmm) REVERT: B 107 MET cc_start: 0.8419 (mtm) cc_final: 0.8120 (ttm) REVERT: B 372 ASP cc_start: 0.9050 (m-30) cc_final: 0.8736 (t0) REVERT: B 386 MET cc_start: 0.8219 (tmm) cc_final: 0.8008 (tmm) REVERT: B 478 ARG cc_start: 0.8844 (tpp-160) cc_final: 0.7813 (ttp80) REVERT: B 614 MET cc_start: 0.9152 (mtp) cc_final: 0.8895 (mtp) REVERT: C 250 MET cc_start: 0.9107 (tpp) cc_final: 0.8822 (mmt) REVERT: E 144 GLU cc_start: 0.9201 (tt0) cc_final: 0.8557 (pt0) REVERT: G 20 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9109 (p) REVERT: G 93 ASP cc_start: 0.8762 (t0) cc_final: 0.8558 (t0) REVERT: G 110 ARG cc_start: 0.8670 (ttm-80) cc_final: 0.8426 (ttm-80) REVERT: G 124 PHE cc_start: 0.8339 (m-80) cc_final: 0.7898 (m-10) REVERT: G 142 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8676 (mmt) REVERT: I 107 MET cc_start: 0.9256 (tpp) cc_final: 0.8495 (tpp) REVERT: I 181 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8591 (mp10) REVERT: I 234 TYR cc_start: 0.8947 (m-80) cc_final: 0.8632 (m-80) REVERT: I 793 PHE cc_start: 0.7571 (t80) cc_final: 0.6822 (t80) REVERT: S 45 MET cc_start: 0.9004 (mmm) cc_final: 0.8526 (mmm) REVERT: S 49 SER cc_start: 0.9496 (t) cc_final: 0.9267 (p) REVERT: S 59 THR cc_start: 0.8478 (p) cc_final: 0.8124 (t) REVERT: S 105 ASP cc_start: 0.8823 (m-30) cc_final: 0.8565 (t0) REVERT: S 115 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8732 (ttmm) REVERT: S 116 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8935 (mm-30) REVERT: S 133 GLU cc_start: 0.8578 (tp30) cc_final: 0.8211 (tp30) REVERT: S 144 TYR cc_start: 0.8460 (m-80) cc_final: 0.7785 (m-80) outliers start: 71 outliers final: 33 residues processed: 291 average time/residue: 0.2067 time to fit residues: 95.3290 Evaluate side-chains 243 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 252 HIS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 259 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 322 optimal weight: 9.9990 chunk 297 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 111 GLN I 776 GLN S 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041998 restraints weight = 100500.649| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.21 r_work: 0.2501 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31546 Z= 0.185 Angle : 0.568 10.669 42682 Z= 0.302 Chirality : 0.044 0.268 4829 Planarity : 0.004 0.043 5361 Dihedral : 6.743 58.967 4300 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.70 % Allowed : 8.74 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3752 helix: 1.33 (0.14), residues: 1380 sheet: -0.61 (0.22), residues: 562 loop : -0.75 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.023 0.001 TYR S 134 PHE 0.032 0.001 PHE A 938 TRP 0.012 0.001 TRP A1054 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (31529) covalent geometry : angle 0.56475 / 0.30 (42662) SS BOND : bond 0.01204 / 0.63 ( 1) SS BOND : angle 3.91172 / 2.61 ( 2) hydrogen bonds : bond 0.04522 / 3.09 ( 1287) hydrogen bonds : angle 4.98943 / 3.46 ( 3651) metal coordination : bond 0.00891 / 0.65 ( 16) metal coordination : angle 2.63494 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8915 (p0) cc_final: 0.8629 (p0) REVERT: A 117 ARG cc_start: 0.9187 (ttm110) cc_final: 0.8770 (mtm110) REVERT: A 122 LYS cc_start: 0.9301 (mtmt) cc_final: 0.9008 (mmmt) REVERT: A 124 LEU cc_start: 0.8915 (mt) cc_final: 0.8645 (pp) REVERT: A 226 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8912 (mmp) REVERT: A 989 GLN cc_start: 0.8787 (mt0) cc_final: 0.8542 (mt0) REVERT: A 1062 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7234 (t0) REVERT: A 1063 GLU cc_start: 0.8866 (pm20) cc_final: 0.8625 (pm20) REVERT: A 1128 MET cc_start: 0.9230 (tpp) cc_final: 0.9024 (tpp) REVERT: A 1247 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9170 (pt) REVERT: B 67 MET cc_start: 0.8592 (mmm) cc_final: 0.8322 (mmm) REVERT: B 107 MET cc_start: 0.8356 (mtm) cc_final: 0.8024 (ttm) REVERT: B 372 ASP cc_start: 0.9104 (m-30) cc_final: 0.8754 (t0) REVERT: B 386 MET cc_start: 0.8293 (tmm) cc_final: 0.8083 (tmm) REVERT: B 478 ARG cc_start: 0.8874 (tpp-160) cc_final: 0.7796 (ttp80) REVERT: B 544 MET cc_start: 0.9071 (mtp) cc_final: 0.8815 (mtp) REVERT: B 614 MET cc_start: 0.9186 (mtp) cc_final: 0.8929 (mtp) REVERT: C 134 LYS cc_start: 0.8317 (ptmm) cc_final: 0.8078 (ttpp) REVERT: C 250 MET cc_start: 0.9071 (tpp) cc_final: 0.8775 (mmt) REVERT: C 304 ARG cc_start: 0.9047 (ptp90) cc_final: 0.8601 (ptp90) REVERT: E 144 GLU cc_start: 0.9168 (tt0) cc_final: 0.8516 (pt0) REVERT: F 109 MET cc_start: 0.9225 (mmt) cc_final: 0.8932 (mmp) REVERT: G 20 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9089 (p) REVERT: G 93 ASP cc_start: 0.8789 (t0) cc_final: 0.8548 (t0) REVERT: G 124 PHE cc_start: 0.8402 (m-80) cc_final: 0.7966 (m-10) REVERT: G 142 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8675 (mmt) REVERT: I 107 MET cc_start: 0.9207 (tpp) cc_final: 0.8420 (tpp) REVERT: I 181 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8595 (mp10) REVERT: I 234 TYR cc_start: 0.8954 (m-80) cc_final: 0.8673 (m-80) REVERT: I 369 ASN cc_start: 0.6468 (OUTLIER) cc_final: 0.6058 (m-40) REVERT: I 790 MET cc_start: 0.9020 (mmt) cc_final: 0.8768 (mmm) REVERT: S 45 MET cc_start: 0.8976 (mmm) cc_final: 0.8522 (mmm) REVERT: S 49 SER cc_start: 0.9548 (t) cc_final: 0.9297 (p) REVERT: S 59 THR cc_start: 0.8449 (p) cc_final: 0.8100 (t) REVERT: S 93 SER cc_start: 0.9439 (m) cc_final: 0.9178 (p) REVERT: S 105 ASP cc_start: 0.8773 (m-30) cc_final: 0.8506 (t0) REVERT: S 115 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8589 (ttmm) REVERT: S 116 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8843 (mm-30) REVERT: S 133 GLU cc_start: 0.8611 (tp30) cc_final: 0.8232 (tp30) REVERT: S 144 TYR cc_start: 0.8529 (m-80) cc_final: 0.7966 (m-80) REVERT: S 149 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8065 (m-40) outliers start: 59 outliers final: 36 residues processed: 262 average time/residue: 0.1970 time to fit residues: 82.1672 Evaluate side-chains 248 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 252 HIS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 297 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 218 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.041905 restraints weight = 99354.824| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.18 r_work: 0.2513 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31546 Z= 0.181 Angle : 0.548 9.808 42682 Z= 0.292 Chirality : 0.044 0.273 4829 Planarity : 0.003 0.041 5361 Dihedral : 6.563 59.381 4293 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.96 % Allowed : 8.94 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3752 helix: 1.46 (0.14), residues: 1368 sheet: -0.54 (0.22), residues: 546 loop : -0.67 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 86 TYR 0.025 0.001 TYR S 134 PHE 0.030 0.001 PHE A 938 TRP 0.012 0.001 TRP A1054 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (31529) covalent geometry : angle 0.54466 / 0.29 (42662) SS BOND : bond 0.00583 / 0.31 ( 1) SS BOND : angle 2.15207 / 1.43 ( 2) hydrogen bonds : bond 0.04319 / 2.95 ( 1287) hydrogen bonds : angle 4.88785 / 3.39 ( 3651) metal coordination : bond 0.00838 / 0.60 ( 16) metal coordination : angle 2.75591 / 1.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 216 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8894 (p0) cc_final: 0.8594 (p0) REVERT: A 122 LYS cc_start: 0.9315 (mtmt) cc_final: 0.9000 (mmmt) REVERT: A 124 LEU cc_start: 0.8933 (mt) cc_final: 0.8668 (pp) REVERT: A 226 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8937 (mmp) REVERT: A 989 GLN cc_start: 0.8781 (mt0) cc_final: 0.8576 (mt0) REVERT: A 1062 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7295 (t0) REVERT: A 1063 GLU cc_start: 0.8825 (pm20) cc_final: 0.8611 (pm20) REVERT: A 1247 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9149 (pt) REVERT: B 107 MET cc_start: 0.8358 (mtm) cc_final: 0.8038 (ttm) REVERT: B 372 ASP cc_start: 0.9122 (m-30) cc_final: 0.8774 (t0) REVERT: B 386 MET cc_start: 0.8311 (tmm) cc_final: 0.8087 (tmm) REVERT: B 478 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.7875 (ttp80) REVERT: B 614 MET cc_start: 0.9156 (mtp) cc_final: 0.8910 (mtp) REVERT: B 879 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8782 (tt) REVERT: C 134 LYS cc_start: 0.8330 (ptmm) cc_final: 0.8052 (ttpp) REVERT: C 250 MET cc_start: 0.9073 (tpp) cc_final: 0.8778 (mmt) REVERT: E 18 GLU cc_start: 0.9501 (tp30) cc_final: 0.9178 (tp30) REVERT: E 55 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8447 (p0) REVERT: E 144 GLU cc_start: 0.9178 (tt0) cc_final: 0.8523 (pt0) REVERT: F 81 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: F 109 MET cc_start: 0.9263 (mmt) cc_final: 0.8924 (mmt) REVERT: G 20 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9080 (p) REVERT: G 83 ASP cc_start: 0.7941 (m-30) cc_final: 0.7735 (m-30) REVERT: G 93 ASP cc_start: 0.8833 (t0) cc_final: 0.8575 (t0) REVERT: G 124 PHE cc_start: 0.8474 (m-80) cc_final: 0.7965 (m-10) REVERT: G 142 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8674 (mmt) REVERT: I 181 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8579 (mp10) REVERT: I 234 TYR cc_start: 0.8962 (m-80) cc_final: 0.8664 (m-80) REVERT: I 342 TYR cc_start: 0.5880 (t80) cc_final: 0.5646 (t80) REVERT: I 790 MET cc_start: 0.9001 (mmt) cc_final: 0.8747 (mmm) REVERT: S 45 MET cc_start: 0.9051 (mmm) cc_final: 0.8575 (mmm) REVERT: S 49 SER cc_start: 0.9547 (t) cc_final: 0.9302 (p) REVERT: S 93 SER cc_start: 0.9430 (m) cc_final: 0.9165 (p) REVERT: S 105 ASP cc_start: 0.8765 (m-30) cc_final: 0.8537 (t0) REVERT: S 116 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8921 (mm-30) REVERT: S 133 GLU cc_start: 0.8679 (tp30) cc_final: 0.8297 (tp30) REVERT: S 144 TYR cc_start: 0.8564 (m-80) cc_final: 0.8148 (m-80) outliers start: 68 outliers final: 38 residues processed: 267 average time/residue: 0.1960 time to fit residues: 84.3404 Evaluate side-chains 245 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 252 HIS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 134 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 1 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 161 GLN S 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.046931 restraints weight = 94174.183| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.13 r_work: 0.2529 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31546 Z= 0.149 Angle : 0.528 11.281 42682 Z= 0.281 Chirality : 0.043 0.275 4829 Planarity : 0.003 0.038 5361 Dihedral : 6.452 59.696 4293 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.62 % Allowed : 9.46 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3752 helix: 1.56 (0.14), residues: 1362 sheet: -0.50 (0.23), residues: 539 loop : -0.60 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 119 TYR 0.024 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.013 0.001 TRP A1054 HIS 0.004 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (31529) covalent geometry : angle 0.52475 / 0.28 (42662) SS BOND : bond 0.02234 / 1.18 ( 1) SS BOND : angle 4.16537 / 2.78 ( 2) hydrogen bonds : bond 0.04086 / 2.79 ( 1287) hydrogen bonds : angle 4.78332 / 3.32 ( 3651) metal coordination : bond 0.00721 / 0.54 ( 16) metal coordination : angle 2.53286 / 1.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8887 (p0) cc_final: 0.8593 (p0) REVERT: A 122 LYS cc_start: 0.9309 (mtmt) cc_final: 0.8988 (mmmt) REVERT: A 124 LEU cc_start: 0.8922 (mt) cc_final: 0.8657 (pp) REVERT: A 226 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8933 (mmp) REVERT: A 989 GLN cc_start: 0.8760 (mt0) cc_final: 0.8505 (mt0) REVERT: A 1062 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7331 (t0) REVERT: A 1063 GLU cc_start: 0.8842 (pm20) cc_final: 0.8598 (pm20) REVERT: A 1247 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9169 (pt) REVERT: B 67 MET cc_start: 0.8555 (mmm) cc_final: 0.8200 (mmm) REVERT: B 107 MET cc_start: 0.8299 (mtm) cc_final: 0.7869 (ttm) REVERT: B 372 ASP cc_start: 0.9146 (m-30) cc_final: 0.8798 (t0) REVERT: B 386 MET cc_start: 0.8344 (tmm) cc_final: 0.8108 (tmm) REVERT: B 478 ARG cc_start: 0.8889 (tpp-160) cc_final: 0.7810 (ttp80) REVERT: B 614 MET cc_start: 0.9100 (mtp) cc_final: 0.8855 (mtp) REVERT: B 629 MET cc_start: 0.9333 (mmm) cc_final: 0.9127 (mmm) REVERT: B 879 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8751 (tt) REVERT: C 134 LYS cc_start: 0.8373 (ptmm) cc_final: 0.8071 (ttpp) REVERT: C 250 MET cc_start: 0.9057 (tpp) cc_final: 0.8758 (mmt) REVERT: E 18 GLU cc_start: 0.9503 (tp30) cc_final: 0.9191 (tp30) REVERT: E 55 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8464 (p0) REVERT: E 144 GLU cc_start: 0.9160 (tt0) cc_final: 0.8510 (pt0) REVERT: F 109 MET cc_start: 0.9274 (mmt) cc_final: 0.8969 (mmt) REVERT: G 20 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9092 (p) REVERT: G 83 ASP cc_start: 0.7973 (m-30) cc_final: 0.7748 (m-30) REVERT: G 93 ASP cc_start: 0.8782 (t0) cc_final: 0.8524 (t70) REVERT: G 124 PHE cc_start: 0.8426 (m-80) cc_final: 0.7877 (m-10) REVERT: G 142 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8682 (mmt) REVERT: I 181 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8609 (mp10) REVERT: I 234 TYR cc_start: 0.8974 (m-80) cc_final: 0.8683 (m-80) REVERT: I 268 LYS cc_start: 0.9118 (mppt) cc_final: 0.8788 (mppt) REVERT: I 790 MET cc_start: 0.8979 (mmt) cc_final: 0.8762 (mmm) REVERT: S 42 GLU cc_start: 0.9476 (tt0) cc_final: 0.9156 (tp30) REVERT: S 45 MET cc_start: 0.9056 (mmm) cc_final: 0.8625 (mmm) REVERT: S 49 SER cc_start: 0.9532 (t) cc_final: 0.9281 (p) REVERT: S 99 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8595 (tm-30) REVERT: S 116 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8874 (mm-30) REVERT: S 133 GLU cc_start: 0.8668 (tp30) cc_final: 0.8255 (tp30) REVERT: S 144 TYR cc_start: 0.8545 (m-80) cc_final: 0.8152 (m-80) outliers start: 56 outliers final: 38 residues processed: 259 average time/residue: 0.2029 time to fit residues: 84.6411 Evaluate side-chains 250 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 134 TYR Chi-restraints excluded: chain S residue 149 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 102 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 582 GLN S 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.042415 restraints weight = 99251.082| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.22 r_work: 0.2533 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31546 Z= 0.138 Angle : 0.523 10.919 42682 Z= 0.277 Chirality : 0.043 0.279 4829 Planarity : 0.003 0.046 5361 Dihedral : 6.308 59.994 4290 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.59 % Allowed : 9.81 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3752 helix: 1.66 (0.14), residues: 1353 sheet: -0.48 (0.22), residues: 549 loop : -0.59 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 126 TYR 0.025 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.013 0.001 TRP A1054 HIS 0.003 0.001 HIS F 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31529) covalent geometry : angle 0.52008 / 0.28 (42662) SS BOND : bond 0.00702 / 0.37 ( 1) SS BOND : angle 2.54601 / 1.70 ( 2) hydrogen bonds : bond 0.04011 / 2.75 ( 1287) hydrogen bonds : angle 4.71432 / 3.27 ( 3651) metal coordination : bond 0.00654 / 0.48 ( 16) metal coordination : angle 2.47030 / 1.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9316 (mtmt) cc_final: 0.8988 (mmmt) REVERT: A 124 LEU cc_start: 0.8894 (mt) cc_final: 0.8628 (pp) REVERT: A 226 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8927 (mmp) REVERT: A 461 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: A 989 GLN cc_start: 0.8784 (mt0) cc_final: 0.8555 (mt0) REVERT: A 1062 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7354 (t0) REVERT: A 1063 GLU cc_start: 0.8842 (pm20) cc_final: 0.8577 (pm20) REVERT: A 1247 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9191 (pt) REVERT: B 67 MET cc_start: 0.8556 (mmm) cc_final: 0.8206 (mmm) REVERT: B 107 MET cc_start: 0.8275 (mtm) cc_final: 0.7877 (ttm) REVERT: B 372 ASP cc_start: 0.9114 (m-30) cc_final: 0.8785 (t0) REVERT: B 386 MET cc_start: 0.8329 (tmm) cc_final: 0.8094 (tmm) REVERT: B 478 ARG cc_start: 0.8846 (tpp-160) cc_final: 0.7812 (ttp80) REVERT: B 614 MET cc_start: 0.9076 (mtp) cc_final: 0.8834 (mtp) REVERT: B 879 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (tt) REVERT: C 134 LYS cc_start: 0.8407 (ptmm) cc_final: 0.8092 (ttpp) REVERT: C 250 MET cc_start: 0.9051 (tpp) cc_final: 0.8752 (mmt) REVERT: E 55 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8527 (p0) REVERT: E 144 GLU cc_start: 0.9170 (tt0) cc_final: 0.8540 (pt0) REVERT: G 20 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9144 (p) REVERT: G 83 ASP cc_start: 0.8034 (m-30) cc_final: 0.7803 (m-30) REVERT: G 93 ASP cc_start: 0.8789 (t0) cc_final: 0.8525 (t70) REVERT: G 124 PHE cc_start: 0.8387 (m-80) cc_final: 0.7843 (m-10) REVERT: G 142 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8710 (mmt) REVERT: I 169 LYS cc_start: 0.8482 (tppt) cc_final: 0.8169 (mtmm) REVERT: I 181 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8595 (mp10) REVERT: I 234 TYR cc_start: 0.9010 (m-80) cc_final: 0.8730 (m-80) REVERT: I 369 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.6018 (m-40) REVERT: I 790 MET cc_start: 0.8991 (mmt) cc_final: 0.8780 (mmm) REVERT: S 45 MET cc_start: 0.9066 (mmm) cc_final: 0.8591 (mmm) REVERT: S 49 SER cc_start: 0.9533 (t) cc_final: 0.9294 (p) REVERT: S 99 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8633 (tm-30) REVERT: S 133 GLU cc_start: 0.8689 (tp30) cc_final: 0.8264 (tp30) REVERT: S 144 TYR cc_start: 0.8530 (m-80) cc_final: 0.7993 (m-80) REVERT: S 149 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7996 (m-40) outliers start: 55 outliers final: 37 residues processed: 252 average time/residue: 0.2140 time to fit residues: 86.4072 Evaluate side-chains 246 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 149 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 116 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 343 optimal weight: 8.9990 chunk 287 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** I 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.041332 restraints weight = 100825.345| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.22 r_work: 0.2500 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 31546 Z= 0.258 Angle : 0.576 10.378 42682 Z= 0.303 Chirality : 0.045 0.280 4829 Planarity : 0.004 0.037 5361 Dihedral : 6.346 59.969 4288 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.82 % Allowed : 9.84 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3752 helix: 1.64 (0.14), residues: 1358 sheet: -0.54 (0.22), residues: 541 loop : -0.59 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 119 TYR 0.026 0.001 TYR S 134 PHE 0.030 0.001 PHE A 938 TRP 0.011 0.001 TRP A1054 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (31529) covalent geometry : angle 0.57299 / 0.30 (42662) SS BOND : bond 0.00728 / 0.38 ( 1) SS BOND : angle 2.39245 / 1.59 ( 2) hydrogen bonds : bond 0.04355 / 2.98 ( 1287) hydrogen bonds : angle 4.76769 / 3.31 ( 3651) metal coordination : bond 0.00989 / 0.68 ( 16) metal coordination : angle 2.63661 / 1.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8851 (p0) cc_final: 0.8553 (p0) REVERT: A 122 LYS cc_start: 0.9311 (mtmt) cc_final: 0.8995 (mmmt) REVERT: A 124 LEU cc_start: 0.8864 (mt) cc_final: 0.8605 (pp) REVERT: A 226 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8982 (mmp) REVERT: A 461 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: A 989 GLN cc_start: 0.8825 (mt0) cc_final: 0.8528 (mt0) REVERT: A 1062 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7321 (t0) REVERT: A 1247 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9094 (pt) REVERT: B 107 MET cc_start: 0.8299 (mtm) cc_final: 0.7868 (ttm) REVERT: B 372 ASP cc_start: 0.9117 (m-30) cc_final: 0.8761 (t0) REVERT: B 478 ARG cc_start: 0.8899 (tpp-160) cc_final: 0.7885 (ttp80) REVERT: B 614 MET cc_start: 0.9129 (mtp) cc_final: 0.8889 (mtp) REVERT: B 879 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8780 (tt) REVERT: B 1043 GLU cc_start: 0.8835 (tt0) cc_final: 0.8507 (tt0) REVERT: C 250 MET cc_start: 0.9078 (tpp) cc_final: 0.8814 (mmm) REVERT: E 55 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8603 (p0) REVERT: E 144 GLU cc_start: 0.9164 (tt0) cc_final: 0.8541 (pt0) REVERT: G 20 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9155 (p) REVERT: G 93 ASP cc_start: 0.8792 (t0) cc_final: 0.8520 (t70) REVERT: G 124 PHE cc_start: 0.8379 (m-80) cc_final: 0.7847 (m-10) REVERT: G 142 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8801 (mmt) REVERT: I 169 LYS cc_start: 0.8552 (tppt) cc_final: 0.8251 (mtmm) REVERT: I 181 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8605 (mp10) REVERT: I 234 TYR cc_start: 0.9026 (m-80) cc_final: 0.8726 (m-80) REVERT: I 369 ASN cc_start: 0.6433 (OUTLIER) cc_final: 0.6035 (m-40) REVERT: I 790 MET cc_start: 0.8983 (mmt) cc_final: 0.8775 (mmm) REVERT: S 45 MET cc_start: 0.9072 (mmm) cc_final: 0.8594 (mmm) REVERT: S 49 SER cc_start: 0.9536 (t) cc_final: 0.9300 (p) REVERT: S 99 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8629 (tm-30) REVERT: S 133 GLU cc_start: 0.8711 (tp30) cc_final: 0.8275 (tp30) REVERT: S 144 TYR cc_start: 0.8558 (m-80) cc_final: 0.7960 (m-80) REVERT: S 149 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7940 (m-40) outliers start: 63 outliers final: 41 residues processed: 251 average time/residue: 0.1951 time to fit residues: 79.7959 Evaluate side-chains 248 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 252 HIS Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 149 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 165 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 237 optimal weight: 0.0070 chunk 16 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 283 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN I 284 HIS S 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.042758 restraints weight = 99797.767| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.24 r_work: 0.2539 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31546 Z= 0.114 Angle : 0.520 10.227 42682 Z= 0.276 Chirality : 0.043 0.287 4829 Planarity : 0.003 0.038 5361 Dihedral : 6.240 59.443 4287 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.53 % Allowed : 10.30 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3752 helix: 1.71 (0.14), residues: 1354 sheet: -0.46 (0.22), residues: 549 loop : -0.55 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 86 TYR 0.025 0.001 TYR S 134 PHE 0.028 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (31529) covalent geometry : angle 0.51602 / 0.28 (42662) SS BOND : bond 0.01171 / 0.62 ( 1) SS BOND : angle 5.02062 / 3.35 ( 2) hydrogen bonds : bond 0.03901 / 2.66 ( 1287) hydrogen bonds : angle 4.64923 / 3.23 ( 3651) metal coordination : bond 0.00605 / 0.45 ( 16) metal coordination : angle 2.48171 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9307 (mtmt) cc_final: 0.8970 (mmmt) REVERT: A 124 LEU cc_start: 0.8857 (mt) cc_final: 0.8598 (pp) REVERT: A 226 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8917 (mmp) REVERT: A 461 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: A 989 GLN cc_start: 0.8790 (mt0) cc_final: 0.8515 (mt0) REVERT: A 1062 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7220 (t70) REVERT: B 67 MET cc_start: 0.8486 (mmm) cc_final: 0.7556 (mmm) REVERT: B 107 MET cc_start: 0.8240 (mtm) cc_final: 0.7848 (ttm) REVERT: B 256 MET cc_start: 0.9021 (mmt) cc_final: 0.8724 (mmm) REVERT: B 372 ASP cc_start: 0.9109 (m-30) cc_final: 0.8786 (t0) REVERT: B 478 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.7866 (ttp80) REVERT: B 614 MET cc_start: 0.9043 (mtp) cc_final: 0.8804 (mtp) REVERT: B 879 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8691 (tt) REVERT: B 1043 GLU cc_start: 0.8791 (tt0) cc_final: 0.8466 (tt0) REVERT: C 134 LYS cc_start: 0.8292 (ptmm) cc_final: 0.8059 (ttpp) REVERT: C 250 MET cc_start: 0.9009 (tpp) cc_final: 0.8732 (mmt) REVERT: E 55 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8600 (p0) REVERT: E 144 GLU cc_start: 0.9185 (tt0) cc_final: 0.8531 (pt0) REVERT: G 20 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9151 (p) REVERT: G 93 ASP cc_start: 0.8852 (t0) cc_final: 0.8581 (t70) REVERT: G 124 PHE cc_start: 0.8357 (m-80) cc_final: 0.7797 (m-10) REVERT: G 142 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8289 (ptm) REVERT: I 169 LYS cc_start: 0.8534 (tppt) cc_final: 0.8279 (mtmm) REVERT: I 181 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8640 (mp10) REVERT: I 234 TYR cc_start: 0.8992 (m-80) cc_final: 0.8740 (m-80) REVERT: I 369 ASN cc_start: 0.6384 (OUTLIER) cc_final: 0.5982 (m-40) REVERT: I 662 ASP cc_start: 0.8521 (m-30) cc_final: 0.8155 (p0) REVERT: S 45 MET cc_start: 0.9058 (mmm) cc_final: 0.8563 (mmm) REVERT: S 49 SER cc_start: 0.9523 (t) cc_final: 0.9281 (p) REVERT: S 99 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8667 (tm-30) REVERT: S 133 GLU cc_start: 0.8706 (tp30) cc_final: 0.8266 (tp30) REVERT: S 144 TYR cc_start: 0.8484 (m-80) cc_final: 0.7929 (m-80) REVERT: S 149 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7959 (m-40) outliers start: 53 outliers final: 36 residues processed: 252 average time/residue: 0.1845 time to fit residues: 75.3575 Evaluate side-chains 247 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 149 ASN Chi-restraints excluded: chain S residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 371 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 348 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 299 ASN B 741 HIS I 776 GLN S 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.042823 restraints weight = 98617.832| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.21 r_work: 0.2553 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31546 Z= 0.120 Angle : 0.525 9.957 42682 Z= 0.274 Chirality : 0.043 0.288 4829 Planarity : 0.003 0.038 5361 Dihedral : 6.122 59.911 4286 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.56 % Allowed : 10.36 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3752 helix: 1.77 (0.14), residues: 1351 sheet: -0.39 (0.22), residues: 547 loop : -0.55 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 86 TYR 0.025 0.001 TYR S 134 PHE 0.028 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31529) covalent geometry : angle 0.51842 / 0.27 (42662) SS BOND : bond 0.01048 / 0.55 ( 1) SS BOND : angle 4.40412 / 2.94 ( 2) hydrogen bonds : bond 0.03796 / 2.59 ( 1287) hydrogen bonds : angle 4.59232 / 3.19 ( 3651) metal coordination : bond 0.00556 / 0.41 ( 16) metal coordination : angle 3.74294 / 2.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9308 (mtmt) cc_final: 0.8967 (mmmt) REVERT: A 124 LEU cc_start: 0.8854 (mt) cc_final: 0.8595 (pp) REVERT: A 226 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8894 (mmp) REVERT: A 461 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 989 GLN cc_start: 0.8783 (mt0) cc_final: 0.8482 (mt0) REVERT: A 1062 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7264 (t70) REVERT: B 9 MET cc_start: 0.9315 (tpp) cc_final: 0.9101 (tpp) REVERT: B 67 MET cc_start: 0.8542 (mmm) cc_final: 0.7621 (mmm) REVERT: B 107 MET cc_start: 0.8239 (mtm) cc_final: 0.7786 (ttm) REVERT: B 372 ASP cc_start: 0.9110 (m-30) cc_final: 0.8785 (t0) REVERT: B 478 ARG cc_start: 0.8873 (tpp-160) cc_final: 0.7848 (ttp80) REVERT: B 614 MET cc_start: 0.9034 (mtp) cc_final: 0.8828 (mtp) REVERT: B 879 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (tt) REVERT: B 1043 GLU cc_start: 0.8810 (tt0) cc_final: 0.8484 (tt0) REVERT: C 134 LYS cc_start: 0.8297 (ptmm) cc_final: 0.8039 (ttpp) REVERT: C 250 MET cc_start: 0.9015 (tpp) cc_final: 0.8732 (mmt) REVERT: E 55 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8075 (p0) REVERT: E 57 MET cc_start: 0.8782 (mmm) cc_final: 0.7969 (mmp) REVERT: E 144 GLU cc_start: 0.9171 (tt0) cc_final: 0.8525 (pt0) REVERT: G 20 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9152 (p) REVERT: G 93 ASP cc_start: 0.8869 (t0) cc_final: 0.8588 (t70) REVERT: G 124 PHE cc_start: 0.8343 (m-80) cc_final: 0.7776 (m-10) REVERT: G 142 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8324 (ptt) REVERT: I 169 LYS cc_start: 0.8540 (tppt) cc_final: 0.8327 (mtmm) REVERT: I 181 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8620 (mp10) REVERT: I 234 TYR cc_start: 0.8998 (m-80) cc_final: 0.8746 (m-80) REVERT: I 369 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.5999 (m-40) REVERT: I 662 ASP cc_start: 0.8467 (m-30) cc_final: 0.8145 (p0) REVERT: J 17 GLU cc_start: 0.9180 (mp0) cc_final: 0.8652 (mp0) REVERT: S 45 MET cc_start: 0.8995 (mmm) cc_final: 0.8510 (mmm) REVERT: S 49 SER cc_start: 0.9517 (t) cc_final: 0.9274 (p) REVERT: S 99 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8572 (tm-30) REVERT: S 100 TYR cc_start: 0.8134 (m-80) cc_final: 0.7786 (m-80) REVERT: S 133 GLU cc_start: 0.8708 (tp30) cc_final: 0.8275 (tp30) REVERT: S 144 TYR cc_start: 0.8480 (m-80) cc_final: 0.7938 (m-80) REVERT: S 149 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (m-40) outliers start: 54 outliers final: 38 residues processed: 251 average time/residue: 0.2001 time to fit residues: 81.2523 Evaluate side-chains 249 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN G 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042352 restraints weight = 98942.094| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.19 r_work: 0.2537 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31546 Z= 0.173 Angle : 0.546 9.898 42682 Z= 0.284 Chirality : 0.044 0.288 4829 Planarity : 0.003 0.038 5361 Dihedral : 6.129 58.523 4286 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.50 % Allowed : 10.68 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3752 helix: 1.75 (0.14), residues: 1355 sheet: -0.40 (0.22), residues: 549 loop : -0.54 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 86 TYR 0.025 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.013 0.001 TRP A1054 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (31529) covalent geometry : angle 0.54066 / 0.28 (42662) SS BOND : bond 0.00993 / 0.52 ( 1) SS BOND : angle 4.08567 / 2.72 ( 2) hydrogen bonds : bond 0.03904 / 2.66 ( 1287) hydrogen bonds : angle 4.60321 / 3.19 ( 3651) metal coordination : bond 0.00696 / 0.50 ( 16) metal coordination : angle 3.33622 / 2.50 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9317 (mtmt) cc_final: 0.8975 (mmmt) REVERT: A 124 LEU cc_start: 0.8854 (mt) cc_final: 0.8595 (pp) REVERT: A 226 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8911 (mmp) REVERT: A 461 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: A 989 GLN cc_start: 0.8798 (mt0) cc_final: 0.8479 (mt0) REVERT: A 1062 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7443 (t0) REVERT: B 9 MET cc_start: 0.9300 (tpp) cc_final: 0.9089 (tpp) REVERT: B 67 MET cc_start: 0.8568 (mmm) cc_final: 0.7657 (mmm) REVERT: B 107 MET cc_start: 0.8270 (mtm) cc_final: 0.7810 (ttm) REVERT: B 256 MET cc_start: 0.9035 (mmt) cc_final: 0.8730 (mmm) REVERT: B 372 ASP cc_start: 0.9117 (m-30) cc_final: 0.8792 (t0) REVERT: B 478 ARG cc_start: 0.8875 (tpp-160) cc_final: 0.7898 (ttp80) REVERT: B 614 MET cc_start: 0.9045 (mtp) cc_final: 0.8843 (mtp) REVERT: B 879 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8730 (tt) REVERT: B 1043 GLU cc_start: 0.8817 (tt0) cc_final: 0.8498 (tt0) REVERT: C 134 LYS cc_start: 0.8318 (ptmm) cc_final: 0.8052 (ttpp) REVERT: C 250 MET cc_start: 0.9025 (tpp) cc_final: 0.8734 (mmt) REVERT: E 55 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8134 (p0) REVERT: E 57 MET cc_start: 0.8818 (mmm) cc_final: 0.8049 (mmp) REVERT: E 144 GLU cc_start: 0.9173 (tt0) cc_final: 0.8534 (pt0) REVERT: G 20 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9153 (p) REVERT: G 93 ASP cc_start: 0.8872 (t0) cc_final: 0.8591 (t70) REVERT: G 110 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: G 124 PHE cc_start: 0.8334 (m-80) cc_final: 0.7769 (m-10) REVERT: G 142 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8330 (ptt) REVERT: I 169 LYS cc_start: 0.8562 (tppt) cc_final: 0.8354 (mtmm) REVERT: I 181 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8639 (mp10) REVERT: I 234 TYR cc_start: 0.9016 (m-80) cc_final: 0.8750 (m-80) REVERT: I 369 ASN cc_start: 0.6398 (OUTLIER) cc_final: 0.6013 (m-40) REVERT: I 662 ASP cc_start: 0.8483 (m-30) cc_final: 0.8197 (p0) REVERT: I 776 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9065 (mp10) REVERT: J 17 GLU cc_start: 0.9183 (mp0) cc_final: 0.8651 (mp0) REVERT: S 45 MET cc_start: 0.9066 (mmm) cc_final: 0.8562 (mmm) REVERT: S 49 SER cc_start: 0.9504 (t) cc_final: 0.9239 (p) REVERT: S 99 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8554 (tm-30) REVERT: S 100 TYR cc_start: 0.8146 (m-80) cc_final: 0.7789 (m-80) REVERT: S 133 GLU cc_start: 0.8724 (tp30) cc_final: 0.8288 (tp30) REVERT: S 144 TYR cc_start: 0.8451 (m-80) cc_final: 0.7883 (m-80) REVERT: S 149 ASN cc_start: 0.8437 (m-40) cc_final: 0.8045 (m110) outliers start: 52 outliers final: 42 residues processed: 244 average time/residue: 0.1926 time to fit residues: 76.0602 Evaluate side-chains 253 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 853 ASN Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 661 HIS Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain S residue 88 TYR Chi-restraints excluded: chain S residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 68 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 338 optimal weight: 9.9990 chunk 117 optimal weight: 0.0980 chunk 135 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN G 100 GLN I 776 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.042162 restraints weight = 100157.499| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.24 r_work: 0.2528 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31546 Z= 0.180 Angle : 0.547 9.684 42682 Z= 0.286 Chirality : 0.044 0.287 4829 Planarity : 0.003 0.038 5361 Dihedral : 6.140 58.243 4286 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.59 % Allowed : 10.70 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3752 helix: 1.75 (0.14), residues: 1356 sheet: -0.38 (0.22), residues: 546 loop : -0.54 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 86 TYR 0.024 0.001 TYR S 134 PHE 0.029 0.001 PHE A 938 TRP 0.015 0.001 TRP I 259 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (31529) covalent geometry : angle 0.54299 / 0.29 (42662) SS BOND : bond 0.00903 / 0.48 ( 1) SS BOND : angle 3.93595 / 2.62 ( 2) hydrogen bonds : bond 0.03999 / 2.73 ( 1287) hydrogen bonds : angle 4.61505 / 3.21 ( 3651) metal coordination : bond 0.00754 / 0.53 ( 16) metal coordination : angle 3.14779 / 2.33 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6161.88 seconds wall clock time: 107 minutes 4.84 seconds (6424.84 seconds total)