Starting phenix.real_space_refine on Fri Sep 27 00:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ap8_11850/09_2024/7ap8_11850.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 41 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 20102 2.51 5 N 5254 2.21 5 O 5968 1.98 5 H 31397 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62909 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 20500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 20500 Classifications: {'peptide': 1268} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1223} Chain: "B" Number of atoms: 18237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 18237 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4954 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "E" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3043 Classifications: {'peptide': 184} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1723 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2373 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7808 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 443} Chain breaks: 3 Chain: "J" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1020 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "N" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 507 Classifications: {'DNA': 16} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 163 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "S" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1909 Classifications: {'peptide': 116} 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: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 667 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 1 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 715 SG CYS A 49 89.848 104.068 62.491 1.00134.69 S ATOM 761 SG CYS A 52 93.581 104.271 61.700 1.00127.43 S ATOM 863 SG CYS A 59 92.110 101.022 63.066 1.00125.18 S ATOM 1391 SG CYS A 90 76.428 101.259 109.420 1.00158.81 S ATOM 1437 SG CYS A 93 77.925 104.709 110.280 1.00165.34 S ATOM 2057 SG CYS A 130 77.710 102.094 112.888 1.00165.82 S ATOM 2131 SG CYS A 135 74.521 103.724 111.732 1.00169.80 S ATOM 37521 SG CYS B1087 100.067 105.568 76.581 1.00115.64 S ATOM 37560 SG CYS B1090 96.557 104.291 77.436 1.00115.35 S ATOM 37740 SG CYS B1103 96.952 106.861 74.829 1.00116.74 S ATOM 37793 SG CYS B1106 97.603 107.882 78.377 1.00121.82 S ATOM 54373 SG CYS I 326 102.610 97.220 38.634 1.00228.96 S ATOM 54977 SG CYS I 363 100.567 93.995 39.544 1.00203.17 S ATOM 55027 SG CYS I 366 104.035 94.588 41.070 1.00198.78 S Time building chain proxies: 22.11, per 1000 atoms: 0.35 Number of scatterers: 62909 At special positions: 0 Unit cell: (164.843, 154.208, 155.271, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 142 16.00 P 41 15.00 Mg 1 11.99 O 5968 8.00 N 5254 7.00 C 20102 6.00 H 31397 1.00 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: 13.52 Conformation dependent library (CDL) restraints added in 4.2 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 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " 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: 148 helices and 47 sheets defined 41.4% alpha, 15.3% beta 15 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 25.49 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 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.711A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 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: 3.807A 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: 3.793A 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 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: 4.064A 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: 3.546A pdb=" N ILE A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.935A 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: 3.648A 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 715 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: 3.719A 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: 3.608A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.587A 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 removed outlier: 3.510A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.192A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (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: 3.517A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.512A pdb=" N ASN A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.186A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 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: 3.681A 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 43 removed outlier: 4.616A pdb=" N PHE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN B 34 " --> pdb=" O PRO B 30 " (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: 3.526A pdb=" N ASN B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.800A pdb=" N ILE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.791A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.795A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.535A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.506A pdb=" N CYS B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.608A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.713A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 4.085A 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: 3.663A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.650A pdb=" N MET B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.665A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 4.024A 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: 3.992A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 732 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: 3.793A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 removed outlier: 4.261A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 941 removed outlier: 4.051A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.651A 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 1054 through 1065 Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.655A 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: 4.053A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.319A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.832A 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 158 removed outlier: 3.643A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) 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 229 removed outlier: 3.902A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.527A 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 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.927A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 removed outlier: 3.535A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 101 removed outlier: 3.900A 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: 3.766A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.534A pdb=" N ILE F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) 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 170 through 186 removed outlier: 6.131A pdb=" N ASP I 180 " --> pdb=" O GLU I 176 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 264 removed outlier: 3.662A pdb=" N ASP I 258 " --> pdb=" O ASN I 254 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.797A 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: 4.085A pdb=" N TYR I 692 " --> pdb=" O LEU I 688 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE I 693 " --> pdb=" O LYS I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 710 removed outlier: 3.555A pdb=" N PHE I 709 " --> pdb=" O TYR I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 723 through 742 Processing helix chain 'I' and resid 756 through 770 removed outlier: 3.598A pdb=" N LYS I 770 " --> pdb=" O ILE I 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 793 removed outlier: 5.515A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 removed outlier: 3.565A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.528A pdb=" N VAL J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.547A 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: 3.535A pdb=" N GLU S 116 " --> pdb=" O GLY S 112 " (cutoff:3.500A) 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: 4.371A 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: 4.399A 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: 3.998A 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: 7.387A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.905A 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: 7.323A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.498A 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 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 removed outlier: 6.497A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB3, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB4, first strand: chain 'A' and resid 1106 through 1107 Processing sheet with id=AB5, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012 Processing sheet with id=AB7, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.726A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.726A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 5.651A pdb=" N ILE B 68 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 57 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.611A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.446A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.779A pdb=" N ILE B 530 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 539 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE B 528 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.787A pdb=" N ILE B 772 " --> pdb=" O ARG B 875 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASP J 61 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.641A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'C' and resid 37 through 43 removed outlier: 5.453A pdb=" N GLY C 38 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE C 144 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL C 40 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 142 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AD9, first strand: chain 'C' and resid 251 through 253 Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 38 Processing sheet with id=AE2, first strand: chain 'E' and resid 63 through 65 removed outlier: 6.415A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.348A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 91 removed outlier: 4.405A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 114 through 116 Processing sheet with id=AE6, first strand: chain 'I' and resid 121 through 123 Processing sheet with id=AE7, first strand: chain 'I' and resid 161 through 166 removed outlier: 6.390A pdb=" N ILE I 128 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE I 164 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 209 through 217 Processing sheet with id=AE9, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AF1, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AF2, first strand: chain 'I' and resid 667 through 670 removed outlier: 4.353A pdb=" N LYS I 667 " --> pdb=" O GLU I 678 " (cutoff:3.500A) 1297 hydrogen bonds defined for protein. 3555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 27.99 Time building geometry restraints manager: 16.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 31352 1.04 - 1.23: 1448 1.23 - 1.43: 12150 1.43 - 1.63: 18459 1.63 - 1.83: 223 Bond restraints: 63632 Sorted by residual: bond pdb=" C1' DT N 55 " pdb=" N1 DT N 55 " ideal model delta sigma weight residual 1.490 1.530 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" C1' DT N 56 " pdb=" N1 DT N 56 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" C1' DC N 51 " pdb=" N1 DC N 51 " ideal model delta sigma weight residual 1.490 1.526 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C1' DC N 50 " pdb=" N1 DC N 50 " ideal model delta sigma weight residual 1.490 1.525 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA ILE I 264 " pdb=" CB ILE I 264 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.37e+00 ... (remaining 63627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 111873 1.42 - 2.83: 3099 2.83 - 4.25: 192 4.25 - 5.67: 57 5.67 - 7.09: 5 Bond angle restraints: 115226 Sorted by residual: angle pdb=" N VAL I 660 " pdb=" CA VAL I 660 " pdb=" C VAL I 660 " ideal model delta sigma weight residual 109.34 103.25 6.09 2.08e+00 2.31e-01 8.56e+00 angle pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" C GLU I 680 " pdb=" N ARG I 681 " pdb=" CA ARG I 681 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" CA GLY A 64 " pdb=" C GLY A 64 " pdb=" N LYS A 65 " ideal model delta sigma weight residual 114.56 117.91 -3.35 1.22e+00 6.72e-01 7.54e+00 angle pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " pdb=" CG PHE A 938 " ideal model delta sigma weight residual 113.80 116.46 -2.66 1.00e+00 1.00e+00 7.09e+00 ... (remaining 115221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 27439 17.29 - 34.58: 1643 34.58 - 51.87: 427 51.87 - 69.16: 180 69.16 - 86.45: 11 Dihedral angle restraints: 29700 sinusoidal: 16437 harmonic: 13263 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 -152.24 66.24 1 1.00e+01 1.00e-02 5.73e+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 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+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 -155.18 -24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 29697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3131 0.032 - 0.065: 1215 0.065 - 0.097: 327 0.097 - 0.129: 247 0.129 - 0.162: 32 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CA ILE B 130 " pdb=" N ILE B 130 " pdb=" C ILE B 130 " pdb=" CB ILE B 130 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ILE I 222 " pdb=" N ILE I 222 " pdb=" C ILE I 222 " pdb=" CB ILE I 222 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 4949 not shown) Planarity restraints: 9050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 856 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ARG B 856 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG B 856 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 857 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 938 " 0.018 2.00e-02 2.50e+03 1.16e-02 4.07e+00 pdb=" CG PHE A 938 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 938 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 938 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 938 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 938 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 938 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 938 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 938 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 938 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 938 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 938 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 546 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C CYS B 546 " -0.031 2.00e-02 2.50e+03 pdb=" O CYS B 546 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 547 " 0.010 2.00e-02 2.50e+03 ... (remaining 9047 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3376 2.21 - 2.81: 133922 2.81 - 3.40: 172864 3.40 - 4.00: 235583 4.00 - 4.60: 364127 Nonbonded interactions: 909872 Sorted by model distance: nonbonded pdb=" O MET I 715 " pdb="HH22 ARG I 757 " model vdw 1.609 2.450 nonbonded pdb=" H CYS B 471 " pdb=" O GLN B 487 " model vdw 1.629 2.450 nonbonded pdb=" O ASN B 376 " pdb="HD22 ASN B 380 " model vdw 1.632 2.450 nonbonded pdb=" O LEU A 517 " pdb=" H ILE A 524 " model vdw 1.669 2.450 nonbonded pdb=" OE1 GLU E 18 " pdb=" HH TYR E 35 " model vdw 1.676 2.450 ... (remaining 909867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.820 Extract box with map and model: 2.010 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 153.970 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.003 0.041 32235 Z= 0.225 Angle : 0.548 7.087 43747 Z= 0.304 Chirality : 0.043 0.162 4952 Planarity : 0.003 0.043 5392 Dihedral : 11.967 86.451 12235 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.76 % Allowed : 3.98 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3752 helix: 1.47 (0.15), residues: 1346 sheet: -0.70 (0.21), residues: 562 loop : -0.68 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.005 0.001 HIS B 318 PHE 0.035 0.001 PHE A 938 TYR 0.021 0.001 TYR S 134 ARG 0.004 0.001 ARG E 163 *********************** 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 439 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 378 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8158 (p0) REVERT: A 791 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9222 (tt) REVERT: A 1056 MET cc_start: 0.8355 (ttt) cc_final: 0.7942 (ttt) REVERT: B 67 MET cc_start: 0.7829 (mmm) cc_final: 0.7234 (mmm) REVERT: B 237 SER cc_start: 0.9429 (m) cc_final: 0.9175 (p) REVERT: B 478 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7845 (ttp80) REVERT: B 784 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 77 MET cc_start: 0.8459 (ttm) cc_final: 0.8258 (ttp) REVERT: C 236 ASN cc_start: 0.8883 (m-40) cc_final: 0.8679 (m110) REVERT: G 20 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9094 (p) REVERT: G 88 THR cc_start: 0.8614 (m) cc_final: 0.8319 (p) REVERT: I 181 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8543 (mm110) REVERT: I 310 ASP cc_start: 0.8413 (t0) cc_final: 0.8072 (p0) REVERT: J 3 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8554 (t80) REVERT: S 42 GLU cc_start: 0.9214 (tt0) cc_final: 0.8968 (tp30) REVERT: S 127 CYS cc_start: 0.7824 (m) cc_final: 0.7422 (m) REVERT: S 133 GLU cc_start: 0.8056 (tp30) cc_final: 0.7746 (tp30) REVERT: S 141 ASP cc_start: 0.8676 (t0) cc_final: 0.8285 (t70) REVERT: S 146 ASP cc_start: 0.8968 (m-30) cc_final: 0.8317 (t0) outliers start: 61 outliers final: 13 residues processed: 428 average time/residue: 1.0962 time to fit residues: 703.0008 Evaluate side-chains 224 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain J residue 3 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 0.0870 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1020 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32235 Z= 0.261 Angle : 0.527 5.845 43747 Z= 0.290 Chirality : 0.042 0.148 4952 Planarity : 0.004 0.055 5392 Dihedral : 11.179 64.843 4630 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.13 % Allowed : 6.38 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3752 helix: 1.56 (0.14), residues: 1349 sheet: -0.72 (0.21), residues: 564 loop : -0.71 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.004 0.001 HIS B 32 PHE 0.027 0.001 PHE A 938 TYR 0.014 0.001 TYR B 38 ARG 0.007 0.000 ARG E 138 *********************** 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 250 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASN cc_start: 0.8305 (t0) cc_final: 0.8013 (t0) REVERT: A 256 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8211 (p0) REVERT: A 972 LYS cc_start: 0.8871 (mttt) cc_final: 0.8628 (mtpp) REVERT: B 67 MET cc_start: 0.7744 (mmm) cc_final: 0.7046 (mmm) REVERT: G 20 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9098 (p) REVERT: G 88 THR cc_start: 0.8570 (m) cc_final: 0.8364 (p) REVERT: I 121 MET cc_start: 0.8452 (mmt) cc_final: 0.8041 (mmt) REVERT: I 181 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8585 (mm110) REVERT: I 310 ASP cc_start: 0.8312 (t0) cc_final: 0.8050 (p0) REVERT: J 3 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8585 (t80) REVERT: S 42 GLU cc_start: 0.9168 (tt0) cc_final: 0.8948 (tp30) REVERT: S 127 CYS cc_start: 0.7468 (m) cc_final: 0.7108 (m) REVERT: S 133 GLU cc_start: 0.8164 (tp30) cc_final: 0.7768 (tp30) REVERT: S 141 ASP cc_start: 0.8694 (t0) cc_final: 0.8335 (t70) REVERT: S 146 ASP cc_start: 0.9003 (m-30) cc_final: 0.8279 (t0) outliers start: 39 outliers final: 25 residues processed: 243 average time/residue: 0.9705 time to fit residues: 365.5556 Evaluate side-chains 220 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 370 optimal weight: 7.9990 chunk 305 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32235 Z= 0.372 Angle : 0.549 5.388 43747 Z= 0.304 Chirality : 0.043 0.154 4952 Planarity : 0.004 0.056 5392 Dihedral : 10.990 62.431 4624 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.36 % Allowed : 7.27 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3752 helix: 1.39 (0.14), residues: 1362 sheet: -0.77 (0.21), residues: 565 loop : -0.86 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 365 HIS 0.004 0.001 HIS B 32 PHE 0.029 0.001 PHE A 938 TYR 0.015 0.001 TYR S 134 ARG 0.006 0.000 ARG G 110 *********************** 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 239 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 192 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8313 (p0) REVERT: B 544 MET cc_start: 0.8500 (ptp) cc_final: 0.8266 (ptp) REVERT: C 250 MET cc_start: 0.9029 (tpp) cc_final: 0.8690 (tpt) REVERT: G 20 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9116 (p) REVERT: G 107 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8735 (mtmm) REVERT: I 181 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8530 (mm110) REVERT: I 258 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.8801 (t0) REVERT: I 310 ASP cc_start: 0.8233 (t0) cc_final: 0.8009 (t70) REVERT: J 3 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8563 (t80) REVERT: S 42 GLU cc_start: 0.9208 (tt0) cc_final: 0.8957 (tp30) REVERT: S 127 CYS cc_start: 0.7650 (m) cc_final: 0.7247 (m) REVERT: S 133 GLU cc_start: 0.8285 (tp30) cc_final: 0.7876 (tp30) REVERT: S 141 ASP cc_start: 0.8731 (t0) cc_final: 0.8278 (t70) outliers start: 47 outliers final: 31 residues processed: 228 average time/residue: 0.9687 time to fit residues: 344.1381 Evaluate side-chains 218 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 258 ASP Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 344 optimal weight: 0.6980 chunk 364 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32235 Z= 0.317 Angle : 0.525 6.745 43747 Z= 0.289 Chirality : 0.043 0.152 4952 Planarity : 0.003 0.057 5392 Dihedral : 10.930 62.873 4624 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.33 % Allowed : 7.62 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3752 helix: 1.47 (0.14), residues: 1357 sheet: -0.81 (0.21), residues: 564 loop : -0.89 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1148 HIS 0.004 0.001 HIS I 661 PHE 0.026 0.001 PHE A 938 TYR 0.014 0.001 TYR S 134 ARG 0.004 0.000 ARG E 138 *********************** 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 235 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7560 (mmm) cc_final: 0.7143 (mtp) REVERT: B 256 MET cc_start: 0.8786 (mmt) cc_final: 0.8354 (mmt) REVERT: B 544 MET cc_start: 0.8443 (ptp) cc_final: 0.8225 (ptp) REVERT: C 250 MET cc_start: 0.9024 (tpp) cc_final: 0.8716 (tpt) REVERT: G 20 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9112 (p) REVERT: G 107 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8762 (mtmm) REVERT: I 181 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8531 (mm110) REVERT: I 258 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.8814 (t0) REVERT: I 310 ASP cc_start: 0.8274 (t0) cc_final: 0.8057 (t70) REVERT: J 3 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8537 (t80) REVERT: S 42 GLU cc_start: 0.9212 (tt0) cc_final: 0.8991 (tp30) REVERT: S 127 CYS cc_start: 0.7705 (m) cc_final: 0.7277 (m) REVERT: S 133 GLU cc_start: 0.8349 (tp30) cc_final: 0.8014 (tp30) REVERT: S 141 ASP cc_start: 0.8739 (t0) cc_final: 0.8289 (t70) outliers start: 46 outliers final: 33 residues processed: 227 average time/residue: 0.9527 time to fit residues: 335.9391 Evaluate side-chains 212 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 258 ASP Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 271 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32235 Z= 0.265 Angle : 0.503 5.287 43747 Z= 0.277 Chirality : 0.042 0.147 4952 Planarity : 0.003 0.065 5392 Dihedral : 10.848 62.789 4622 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.44 % Allowed : 7.67 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3752 helix: 1.55 (0.14), residues: 1359 sheet: -0.82 (0.21), residues: 565 loop : -0.86 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 365 HIS 0.003 0.001 HIS B 32 PHE 0.026 0.001 PHE A 938 TYR 0.014 0.001 TYR S 134 ARG 0.011 0.000 ARG A 349 *********************** 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 229 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7506 (mmm) cc_final: 0.7123 (mtp) REVERT: B 116 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7910 (tppt) REVERT: B 256 MET cc_start: 0.8776 (mmt) cc_final: 0.8333 (mmt) REVERT: B 544 MET cc_start: 0.8484 (ptp) cc_final: 0.8280 (ptp) REVERT: B 879 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 1158 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9018 (mp) REVERT: C 250 MET cc_start: 0.8998 (tpp) cc_final: 0.8695 (tpt) REVERT: G 20 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9116 (p) REVERT: I 181 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8521 (mm110) REVERT: I 310 ASP cc_start: 0.8278 (t0) cc_final: 0.8069 (t70) REVERT: J 3 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8449 (t80) REVERT: S 42 GLU cc_start: 0.9230 (tt0) cc_final: 0.8991 (tp30) REVERT: S 127 CYS cc_start: 0.7739 (m) cc_final: 0.7368 (m) REVERT: S 133 GLU cc_start: 0.8313 (tp30) cc_final: 0.7964 (tp30) REVERT: S 141 ASP cc_start: 0.8762 (t0) cc_final: 0.8492 (t70) outliers start: 50 outliers final: 40 residues processed: 223 average time/residue: 0.9025 time to fit residues: 316.6786 Evaluate side-chains 213 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32235 Z= 0.266 Angle : 0.502 6.417 43747 Z= 0.277 Chirality : 0.042 0.152 4952 Planarity : 0.003 0.055 5392 Dihedral : 10.797 63.083 4622 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.44 % Allowed : 7.91 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3752 helix: 1.58 (0.14), residues: 1366 sheet: -0.81 (0.21), residues: 565 loop : -0.86 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 365 HIS 0.003 0.001 HIS B 32 PHE 0.025 0.001 PHE A 938 TYR 0.014 0.001 TYR C 170 ARG 0.008 0.000 ARG A 349 *********************** 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 227 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7541 (mmm) cc_final: 0.7203 (mtp) REVERT: B 116 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7899 (tppt) REVERT: B 256 MET cc_start: 0.8785 (mmt) cc_final: 0.8331 (mmt) REVERT: B 879 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 1158 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9007 (mp) REVERT: C 250 MET cc_start: 0.8982 (tpp) cc_final: 0.8670 (tpt) REVERT: G 20 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9115 (p) REVERT: I 181 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8512 (mm110) REVERT: J 3 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8450 (t80) REVERT: S 42 GLU cc_start: 0.9232 (tt0) cc_final: 0.8995 (tp30) REVERT: S 127 CYS cc_start: 0.7749 (m) cc_final: 0.7379 (m) REVERT: S 133 GLU cc_start: 0.8326 (tp30) cc_final: 0.8007 (tp30) REVERT: S 141 ASP cc_start: 0.8795 (t0) cc_final: 0.8509 (t70) outliers start: 50 outliers final: 41 residues processed: 220 average time/residue: 0.9024 time to fit residues: 314.1509 Evaluate side-chains 217 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 363 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 641 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN G 37 HIS ** I 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 32235 Z= 0.499 Angle : 0.590 6.762 43747 Z= 0.328 Chirality : 0.044 0.162 4952 Planarity : 0.004 0.056 5392 Dihedral : 10.866 63.876 4622 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.56 % Allowed : 8.11 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3752 helix: 1.24 (0.14), residues: 1374 sheet: -0.87 (0.21), residues: 566 loop : -1.05 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 365 HIS 0.005 0.001 HIS I 724 PHE 0.028 0.002 PHE A 938 TYR 0.015 0.001 TYR S 134 ARG 0.007 0.001 ARG B 853 *********************** 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 226 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: B 116 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7933 (tppt) REVERT: B 256 MET cc_start: 0.8901 (mmt) cc_final: 0.8444 (mmt) REVERT: B 879 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8699 (tt) REVERT: B 1158 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9023 (mp) REVERT: C 250 MET cc_start: 0.8988 (tpp) cc_final: 0.8686 (tpt) REVERT: G 20 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9105 (p) REVERT: I 181 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8513 (mm110) REVERT: I 793 PHE cc_start: 0.6435 (t80) cc_final: 0.5685 (t80) REVERT: J 3 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8558 (t80) REVERT: S 42 GLU cc_start: 0.9241 (tt0) cc_final: 0.8997 (tp30) REVERT: S 46 GLU cc_start: 0.8902 (tp30) cc_final: 0.8684 (tp30) REVERT: S 127 CYS cc_start: 0.7771 (m) cc_final: 0.7383 (m) REVERT: S 133 GLU cc_start: 0.8398 (tp30) cc_final: 0.8100 (tp30) outliers start: 54 outliers final: 46 residues processed: 216 average time/residue: 0.9084 time to fit residues: 310.1646 Evaluate side-chains 219 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU 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 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32235 Z= 0.166 Angle : 0.496 8.001 43747 Z= 0.270 Chirality : 0.042 0.153 4952 Planarity : 0.003 0.054 5392 Dihedral : 10.766 64.382 4619 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.21 % Allowed : 8.57 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3752 helix: 1.68 (0.14), residues: 1358 sheet: -0.81 (0.21), residues: 563 loop : -0.85 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.003 0.001 HIS B 318 PHE 0.023 0.001 PHE A 938 TYR 0.013 0.001 TYR S 134 ARG 0.005 0.000 ARG B 478 *********************** 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 216 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7874 (tppt) REVERT: B 879 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 1158 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8987 (mp) REVERT: C 250 MET cc_start: 0.8987 (tpp) cc_final: 0.8683 (tpt) REVERT: G 20 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9131 (p) REVERT: I 181 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8492 (mm110) REVERT: J 3 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8446 (t80) REVERT: S 42 GLU cc_start: 0.9245 (tt0) cc_final: 0.8993 (tp30) REVERT: S 127 CYS cc_start: 0.7845 (m) cc_final: 0.7443 (m) REVERT: S 133 GLU cc_start: 0.8338 (tp30) cc_final: 0.8045 (tp30) REVERT: S 141 ASP cc_start: 0.8783 (t70) cc_final: 0.8539 (t70) outliers start: 42 outliers final: 38 residues processed: 210 average time/residue: 0.9478 time to fit residues: 315.3515 Evaluate side-chains 211 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 320 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32235 Z= 0.334 Angle : 0.522 7.304 43747 Z= 0.288 Chirality : 0.042 0.151 4952 Planarity : 0.003 0.054 5392 Dihedral : 10.745 64.556 4619 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.38 % Allowed : 8.31 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3752 helix: 1.59 (0.14), residues: 1363 sheet: -0.83 (0.21), residues: 564 loop : -0.92 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 365 HIS 0.003 0.001 HIS A 385 PHE 0.026 0.001 PHE A 938 TYR 0.014 0.001 TYR S 134 ARG 0.005 0.000 ARG B 478 *********************** 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 216 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8434 (t70) REVERT: B 116 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7933 (tppt) REVERT: B 1158 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8999 (mp) REVERT: C 250 MET cc_start: 0.8980 (tpp) cc_final: 0.8666 (tpt) REVERT: G 20 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9111 (p) REVERT: I 181 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8487 (mm110) REVERT: J 3 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8490 (t80) REVERT: S 42 GLU cc_start: 0.9245 (tt0) cc_final: 0.8995 (tp30) REVERT: S 127 CYS cc_start: 0.7775 (m) cc_final: 0.7382 (m) REVERT: S 133 GLU cc_start: 0.8343 (tp30) cc_final: 0.8046 (tp30) outliers start: 48 outliers final: 40 residues processed: 209 average time/residue: 0.9829 time to fit residues: 326.2453 Evaluate side-chains 211 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 375 optimal weight: 7.9990 chunk 345 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 32235 Z= 0.412 Angle : 0.565 7.114 43747 Z= 0.311 Chirality : 0.043 0.157 4952 Planarity : 0.004 0.054 5392 Dihedral : 10.799 65.264 4619 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.44 % Allowed : 8.28 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3752 helix: 1.36 (0.14), residues: 1372 sheet: -0.88 (0.21), residues: 554 loop : -1.03 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.007 0.001 HIS A 385 PHE 0.027 0.002 PHE A 938 TYR 0.014 0.001 TYR B 377 ARG 0.005 0.000 ARG B 853 ********************** 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 215 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 4.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8423 (t70) REVERT: B 1158 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9009 (mp) REVERT: C 250 MET cc_start: 0.9011 (tpp) cc_final: 0.8709 (tpt) REVERT: G 20 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9098 (p) REVERT: I 181 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8466 (mm110) REVERT: I 221 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (m) REVERT: J 3 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8485 (t80) REVERT: S 42 GLU cc_start: 0.9232 (tt0) cc_final: 0.8994 (tp30) REVERT: S 127 CYS cc_start: 0.7821 (m) cc_final: 0.7373 (m) REVERT: S 133 GLU cc_start: 0.8400 (tp30) cc_final: 0.8094 (tp30) outliers start: 50 outliers final: 43 residues processed: 208 average time/residue: 0.9242 time to fit residues: 305.4625 Evaluate side-chains 214 residues out of total 3467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 GLU 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 1123 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 293 ARG Chi-restraints excluded: chain I residue 300 LYS Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain S residue 98 LEU Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 299 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045676 restraints weight = 302894.066| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.17 r_work: 0.2640 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32235 Z= 0.144 Angle : 0.493 8.291 43747 Z= 0.268 Chirality : 0.042 0.155 4952 Planarity : 0.003 0.053 5392 Dihedral : 10.709 65.465 4619 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.27 % Allowed : 8.60 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3752 helix: 1.68 (0.14), residues: 1369 sheet: -0.83 (0.22), residues: 553 loop : -0.87 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.003 0.001 HIS A 385 PHE 0.024 0.001 PHE A 938 TYR 0.013 0.001 TYR S 134 ARG 0.004 0.000 ARG B 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9728.61 seconds wall clock time: 168 minutes 54.79 seconds (10134.79 seconds total)