Starting phenix.real_space_refine on Sat Aug 8 09:47:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9f_37367/08_2026/8w9f_37367.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16800 2.51 5 N 4889 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 277 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "c" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "g" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "j" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "G" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 570 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 92.341 97.136 91.981 1.00 63.46 S ATOM 5555 SG CYS E 266 89.928 95.114 93.570 1.00 53.02 S ATOM 5708 SG CYS E 286 93.231 93.681 92.999 1.00 38.07 S ATOM 5619 SG CYS E 275 100.350 102.730 82.033 1.00 87.52 S ATOM 5640 SG CYS E 278 96.846 101.994 81.535 1.00 89.24 S ATOM 5843 SG CYS E 303 98.070 98.765 80.999 1.00 84.64 S ATOM 5866 SG CYS E 306 98.964 101.341 78.710 1.00 85.05 S ATOM 6956 SG CYS E 440 60.182 85.037 111.606 1.00 27.99 S ATOM 6982 SG CYS E 443 58.098 82.201 111.670 1.00 23.37 S ATOM 7170 SG CYS E 466 59.127 83.512 115.391 1.00 25.28 S ATOM 6795 SG CYS E 420 53.575 85.172 126.282 1.00 30.63 S ATOM 7051 SG CYS E 451 57.050 84.408 125.918 1.00 26.14 S ATOM 14065 SG CYS F 263 43.423 37.948 66.888 1.00 95.21 S ATOM 14082 SG CYS F 266 44.744 34.700 67.224 1.00 88.26 S ATOM 14235 SG CYS F 286 42.230 36.473 69.982 1.00 90.91 S ATOM 14146 SG CYS F 275 40.471 50.443 63.991 1.00 96.38 S ATOM 14167 SG CYS F 278 43.804 49.392 64.497 1.00 89.68 S ATOM 14370 SG CYS F 303 43.056 49.359 68.089 1.00 96.28 S ATOM 14393 SG CYS F 306 42.764 52.457 65.952 1.00 88.14 S Time building chain proxies: 6.07, per 1000 atoms: 0.22 Number of scatterers: 27868 At special positions: 0 Unit cell: (144.571, 183.703, 168.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 104 16.00 P 292 15.00 O 5776 8.00 N 4889 7.00 C 16800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 266 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 263 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 306 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 278 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 18 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 22 sheets defined 60.5% alpha, 4.7% beta 145 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 663 through 677 removed outlier: 3.543A pdb=" N THR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.535A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.748A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.506A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.767A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 removed outlier: 3.578A pdb=" N ASN A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 925 Proline residue: A 892 - end of helix removed outlier: 4.978A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.501A pdb=" N LEU A 933 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.899A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.859A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1064 through 1070 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.626A pdb=" N ASN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 5.041A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.833A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.753A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1237 through 1240 Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.768A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 removed outlier: 3.509A pdb=" N ALA A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.593A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1343 removed outlier: 3.992A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.547A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.731A pdb=" N ASN E 433 " --> pdb=" O HIS E 430 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 434' Processing helix chain 'E' and resid 543 through 580 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.148A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.703A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.622A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.849A pdb=" N LYS B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.580A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 301 removed outlier: 4.425A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 271 through 297 removed outlier: 5.390A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.923A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 348 through 369 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.536A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 4.171A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.764A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 375 removed outlier: 3.716A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 removed outlier: 3.565A pdb=" N ASP D 384 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.576A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 344 removed outlier: 4.647A pdb=" N LYS F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 544 through 577 removed outlier: 3.606A pdb=" N LEU F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.898A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.585A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.539A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.839A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.670A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN c 73 " --> pdb=" O ALA c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.645A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 removed outlier: 3.569A pdb=" N LEU c 115 " --> pdb=" O GLN c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 removed outlier: 3.719A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 124 removed outlier: 4.104A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 3.897A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER e 57 " --> pdb=" O ARG e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.583A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.540A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG f 67 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.531A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.694A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.595A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 124 removed outlier: 3.752A pdb=" N SER h 123 " --> pdb=" O THR h 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.610A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 178 through 179 removed outlier: 3.808A pdb=" N GLU B 62 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'E' and resid 521 through 522 removed outlier: 6.181A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB2, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.140A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 removed outlier: 3.719A pdb=" N ILE c 78 " --> pdb=" O GLY d 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.680A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.608A pdb=" N ILE g 78 " --> pdb=" O GLY h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.853A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 698 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.45: 13581 1.45 - 1.77: 15291 1.77 - 2.08: 159 2.08 - 2.40: 1 2.40 - 2.72: 1 Bond restraints: 29033 Sorted by residual: bond pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 1.512 2.718 -1.206 2.20e-02 2.07e+03 3.00e+03 bond pdb=" CE3 TRP D 236 " pdb=" CZ3 TRP D 236 " ideal model delta sigma weight residual 1.382 2.269 -0.887 3.00e-02 1.11e+03 8.74e+02 bond pdb=" CE2 TRP D 236 " pdb=" CZ2 TRP D 236 " ideal model delta sigma weight residual 1.394 1.823 -0.429 2.10e-02 2.27e+03 4.18e+02 bond pdb=" CZ3 TRP D 236 " pdb=" CH2 TRP D 236 " ideal model delta sigma weight residual 1.400 1.853 -0.453 2.50e-02 1.60e+03 3.28e+02 bond pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 1.466 1.690 -0.224 1.24e-02 6.50e+03 3.26e+02 ... (remaining 29028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.48: 40342 6.48 - 12.96: 90 12.96 - 19.44: 13 19.44 - 25.92: 1 25.92 - 32.40: 1 Bond angle restraints: 40447 Sorted by residual: angle pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta sigma weight residual 109.65 142.05 -32.40 1.74e+00 3.30e-01 3.47e+02 angle pdb=" C LEU c 116 " pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 119.78 138.57 -18.79 1.03e+00 9.43e-01 3.33e+02 angle pdb=" C LYS B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.89 134.57 -14.68 1.02e+00 9.61e-01 2.07e+02 angle pdb=" C LYS B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta sigma weight residual 119.87 133.85 -13.98 1.04e+00 9.25e-01 1.81e+02 angle pdb=" CA TYR F 372 " pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 113.90 136.95 -23.05 1.80e+00 3.09e-01 1.64e+02 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12580 17.88 - 35.77: 2320 35.77 - 53.65: 1420 53.65 - 71.53: 475 71.53 - 89.42: 43 Dihedral angle restraints: 16838 sinusoidal: 8930 harmonic: 7908 Sorted by residual: dihedral pdb=" C ARG E 384 " pdb=" N ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual -122.60 -155.40 32.80 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" C THR E 169 " pdb=" N THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual -122.00 -152.32 30.32 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual 123.40 151.08 -27.68 0 2.50e+00 1.60e-01 1.23e+02 ... (remaining 16835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4425 0.239 - 0.479: 32 0.479 - 0.718: 5 0.718 - 0.957: 2 0.957 - 1.197: 2 Chirality restraints: 4466 Sorted by residual: chirality pdb=" CA THR E 169 " pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CB THR E 169 " both_signs ideal model delta sigma weight residual False 2.53 1.33 1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" CA ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA ASP E 383 " pdb=" N ASP E 383 " pdb=" C ASP E 383 " pdb=" CB ASP E 383 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 4463 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 157 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C ALA B 157 " -0.101 2.00e-02 2.50e+03 pdb=" O ALA B 157 " 0.039 2.00e-02 2.50e+03 pdb=" N SER B 158 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 66 " 0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C ALA B 66 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA B 66 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 470 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 471 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 471 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 471 " 0.061 5.00e-02 4.00e+02 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 10 1.91 - 2.65: 757 2.65 - 3.40: 37779 3.40 - 4.15: 71081 4.15 - 4.90: 119842 Nonbonded interactions: 229469 Sorted by model distance: nonbonded pdb=" CB SER E 179 " pdb=" OE2 GLU B 129 " model vdw 1.158 3.440 nonbonded pdb=" OE2 GLU A 904 " pdb=" ND2 ASN E 116 " model vdw 1.174 3.120 nonbonded pdb=" NZ LYS B 41 " pdb=" SD MET B 315 " model vdw 1.548 3.480 nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.581 3.860 nonbonded pdb=" O SER E 179 " pdb=" OE1 GLU B 129 " model vdw 1.728 3.040 ... (remaining 229464 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 24 through 102) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = (chain 'i' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'j' and (resid -73 through -1 or resid 1 through 73)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4118 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 : 0.013 1.206 29056 Z= 0.732 Angle : 1.145 53.767 40465 Z= 0.758 Chirality : 0.067 1.197 4466 Planarity : 0.006 0.114 4129 Dihedral : 24.101 89.417 11728 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.57 % Favored : 94.90 % Rotamer: Outliers : 7.51 % Allowed : 16.82 % Favored : 75.67 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 2646 helix: -0.63 (0.12), residues: 1500 sheet: -1.14 (0.45), residues: 125 loop : -2.46 (0.16), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 98 TYR 0.053 0.002 TYR G 100 PHE 0.048 0.002 PHE E 387 TRP 0.051 0.004 TRP G 31 HIS 0.009 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01270 / 0.72 (29033) covalent geometry : angle 1.04101 / 0.75 (40447) hydrogen bonds : bond 0.13941 / 9.25 ( 1499) hydrogen bonds : angle 5.67426 / 3.99 ( 4070) metal coordination : bond 0.15145 / 8.50 ( 23) metal coordination : angle 22.58577 / 11.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 457 time to evaluate : 0.698 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: A 778 LEU cc_start: 0.6060 (mm) cc_final: 0.5121 (mm) REVERT: A 903 GLU cc_start: 0.1730 (OUTLIER) cc_final: 0.0963 (mt-10) REVERT: A 1065 LEU cc_start: -0.4742 (OUTLIER) cc_final: -0.5545 (mp) REVERT: A 1332 ASP cc_start: 0.0726 (t0) cc_final: 0.0450 (m-30) REVERT: A 1345 HIS cc_start: -0.1068 (t-90) cc_final: -0.1315 (m170) REVERT: E 108 VAL cc_start: 0.2626 (OUTLIER) cc_final: 0.2253 (m) REVERT: E 123 ILE cc_start: -0.1158 (OUTLIER) cc_final: -0.1536 (mm) REVERT: E 272 PHE cc_start: 0.2359 (OUTLIER) cc_final: 0.2003 (p90) REVERT: E 387 PHE cc_start: 0.1003 (OUTLIER) cc_final: 0.0558 (p90) REVERT: E 388 ASN cc_start: 0.2422 (OUTLIER) cc_final: 0.1933 (t0) REVERT: B 2 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.3197 (t) REVERT: B 14 LYS cc_start: -0.0227 (OUTLIER) cc_final: -0.1078 (mtpt) REVERT: B 32 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.0791 (m-80) REVERT: B 38 HIS cc_start: 0.3201 (OUTLIER) cc_final: 0.2342 (m170) REVERT: B 93 ASN cc_start: 0.3600 (p0) cc_final: 0.3357 (p0) REVERT: B 111 PRO cc_start: -0.0664 (OUTLIER) cc_final: -0.0937 (Cg_exo) REVERT: B 112 VAL cc_start: 0.1354 (OUTLIER) cc_final: 0.0973 (m) REVERT: B 187 VAL cc_start: 0.5049 (p) cc_final: 0.4335 (p) REVERT: B 204 MET cc_start: 0.3062 (ttt) cc_final: 0.2679 (ttm) REVERT: C 222 LEU cc_start: 0.0502 (OUTLIER) cc_final: 0.0093 (tp) REVERT: C 235 ASP cc_start: -0.1351 (OUTLIER) cc_final: -0.2217 (t0) REVERT: C 241 LYS cc_start: -0.0647 (OUTLIER) cc_final: -0.1225 (mttt) REVERT: C 376 ASP cc_start: -0.1499 (OUTLIER) cc_final: -0.2451 (p0) REVERT: D 332 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.1976 (mp) REVERT: F 343 ILE cc_start: 0.0584 (mt) cc_final: -0.0316 (mp) REVERT: a 86 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7964 (t) REVERT: a 89 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (m) REVERT: b 58 LEU cc_start: 0.8296 (tp) cc_final: 0.8077 (tt) REVERT: b 88 TYR cc_start: 0.6500 (m-10) cc_final: 0.6234 (m-10) REVERT: c 30 VAL cc_start: 0.8496 (t) cc_final: 0.8203 (p) REVERT: c 62 ILE cc_start: 0.8790 (tt) cc_final: 0.8213 (mt) REVERT: c 90 ASP cc_start: 0.7134 (t0) cc_final: 0.6913 (t0) REVERT: c 107 VAL cc_start: 0.8332 (m) cc_final: 0.8056 (t) REVERT: d 79 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7806 (mmm160) REVERT: e 87 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8411 (t) REVERT: f 84 MET cc_start: 0.7618 (mmm) cc_final: 0.6642 (tpp) REVERT: h 83 TYR cc_start: 0.7780 (m-10) cc_final: 0.7363 (m-10) REVERT: h 101 LEU cc_start: 0.8847 (mt) cc_final: 0.8413 (tp) outliers start: 180 outliers final: 25 residues processed: 607 average time/residue: 0.1949 time to fit residues: 180.6321 Evaluate side-chains 231 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A 930 HIS A 965 HIS A1004 ASN A1081 ASN A1315 GLN E 304 ASN E 314 ASN E 346 HIS E 347 ASN E 376 ASN E 495 GLN E 541 GLN E 545 ASN E 580 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN C 380 ASN C 389 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 375 ASN D 380 ASN D 393 GLN F 302 HIS F 346 HIS F 355 ASN d 49 HIS d 82 HIS d 95 GLN e 125 GLN f 25 ASN f 93 GLN G 18 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.088718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.062678 restraints weight = 254430.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.064263 restraints weight = 143138.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.064991 restraints weight = 97073.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.066018 restraints weight = 77452.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.066368 restraints weight = 65170.735| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.470 Angle : 0.798 22.836 40465 Z= 0.434 Chirality : 0.047 0.295 4466 Planarity : 0.006 0.111 4129 Dihedral : 26.476 89.719 6239 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 0.38 % Allowed : 3.59 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2646 helix: 0.64 (0.13), residues: 1528 sheet: -0.64 (0.45), residues: 118 loop : -2.15 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 182 TYR 0.050 0.002 TYR E 514 PHE 0.024 0.002 PHE g 25 TRP 0.044 0.003 TRP D 236 HIS 0.041 0.002 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01070 / 0.47 (29033) covalent geometry : angle 0.78732 / 0.43 (40447) hydrogen bonds : bond 0.06132 / 3.98 ( 1499) hydrogen bonds : angle 4.46354 / 3.11 ( 4070) metal coordination : bond 0.02290 / 1.44 ( 23) metal coordination : angle 6.25358 / 3.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 257 time to evaluate : 0.868 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: A 706 VAL cc_start: 0.5917 (t) cc_final: 0.5615 (m) REVERT: A 939 ASP cc_start: 0.4606 (m-30) cc_final: 0.4304 (p0) REVERT: A 948 LEU cc_start: 0.6568 (mp) cc_final: 0.6357 (mm) REVERT: A 1151 TRP cc_start: 0.7041 (t-100) cc_final: 0.6813 (t-100) REVERT: A 1345 HIS cc_start: -0.0837 (t-90) cc_final: -0.1512 (m170) REVERT: E 428 TRP cc_start: 0.1413 (m100) cc_final: 0.1209 (m100) REVERT: B 38 HIS cc_start: 0.4431 (p-80) cc_final: 0.3889 (m170) REVERT: B 247 TYR cc_start: 0.8203 (t80) cc_final: 0.7878 (t80) REVERT: D 387 TYR cc_start: -0.0511 (m-80) cc_final: -0.0843 (m-10) REVERT: F 257 PHE cc_start: -0.0773 (m-10) cc_final: -0.1025 (m-80) REVERT: b 84 MET cc_start: 0.6998 (tpp) cc_final: 0.6570 (tpp) REVERT: b 88 TYR cc_start: 0.6626 (m-10) cc_final: 0.5916 (m-10) REVERT: c 38 ASN cc_start: 0.8529 (m110) cc_final: 0.8217 (m-40) REVERT: c 62 ILE cc_start: 0.8870 (tt) cc_final: 0.8482 (mt) REVERT: c 90 ASP cc_start: 0.7440 (t0) cc_final: 0.7029 (t0) REVERT: f 35 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8133 (mtp85) REVERT: f 84 MET cc_start: 0.6501 (mmm) cc_final: 0.6277 (tpp) outliers start: 9 outliers final: 3 residues processed: 265 average time/residue: 0.1861 time to fit residues: 77.0697 Evaluate side-chains 160 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 191 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 chunk 271 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 169 optimal weight: 0.0010 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS E 347 ASN E 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS d 82 HIS f 75 HIS f 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.087715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.061761 restraints weight = 257626.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.063533 restraints weight = 145224.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.064630 restraints weight = 98642.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.065331 restraints weight = 76923.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.065770 restraints weight = 65437.686| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.207 29056 Z= 0.458 Angle : 0.714 22.976 40465 Z= 0.395 Chirality : 0.044 0.333 4466 Planarity : 0.005 0.099 4129 Dihedral : 26.395 87.495 6239 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2646 helix: 1.07 (0.13), residues: 1527 sheet: -0.54 (0.44), residues: 117 loop : -1.78 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 182 TYR 0.029 0.002 TYR A 675 PHE 0.035 0.002 PHE A1301 TRP 0.044 0.002 TRP D 236 HIS 0.008 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.46 (29033) covalent geometry : angle 0.70881 / 0.39 (40447) hydrogen bonds : bond 0.05208 / 3.42 ( 1499) hydrogen bonds : angle 4.16323 / 2.92 ( 4070) metal coordination : bond 0.00920 / 0.63 ( 23) metal coordination : angle 4.10523 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.921 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: A 939 ASP cc_start: 0.4652 (m-30) cc_final: 0.4393 (p0) REVERT: A 1151 TRP cc_start: 0.7069 (t-100) cc_final: 0.6849 (t-100) REVERT: B 38 HIS cc_start: 0.4369 (p-80) cc_final: 0.3957 (m170) REVERT: D 387 TYR cc_start: -0.0541 (m-80) cc_final: -0.0840 (m-10) REVERT: a 120 MET cc_start: 0.7927 (mtm) cc_final: 0.7404 (ptp) REVERT: c 38 ASN cc_start: 0.8601 (m110) cc_final: 0.8261 (m-40) REVERT: c 90 ASP cc_start: 0.7692 (t0) cc_final: 0.7405 (t0) REVERT: d 62 MET cc_start: 0.8651 (mmm) cc_final: 0.8390 (mmm) REVERT: e 90 MET cc_start: 0.7972 (mmt) cc_final: 0.7734 (mmm) REVERT: e 120 MET cc_start: 0.7936 (mtp) cc_final: 0.7719 (tpp) REVERT: f 84 MET cc_start: 0.6886 (mmm) cc_final: 0.6624 (tpp) REVERT: g 56 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8168 (mt-10) REVERT: h 62 MET cc_start: 0.8483 (mmm) cc_final: 0.8192 (mmm) REVERT: h 101 LEU cc_start: 0.8852 (mm) cc_final: 0.8615 (tp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1738 time to fit residues: 58.5476 Evaluate side-chains 141 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 268 optimal weight: 40.0000 chunk 20 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS A 921 GLN A1137 ASN A1234 ASN E 350 GLN E 352 GLN E 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS c 38 ASN c 84 GLN f 93 GLN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.086412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.060462 restraints weight = 257011.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.062107 restraints weight = 145931.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.063187 restraints weight = 100146.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.063861 restraints weight = 78200.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.064270 restraints weight = 66829.741| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.463 Angle : 0.714 23.155 40465 Z= 0.395 Chirality : 0.044 0.204 4466 Planarity : 0.005 0.086 4129 Dihedral : 26.479 86.487 6239 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2646 helix: 1.02 (0.13), residues: 1532 sheet: -0.66 (0.42), residues: 123 loop : -1.76 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 564 TYR 0.028 0.002 TYR g 50 PHE 0.026 0.002 PHE e 104 TRP 0.044 0.002 TRP D 236 HIS 0.023 0.002 HIS C 369 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.46 (29033) covalent geometry : angle 0.71090 / 0.39 (40447) hydrogen bonds : bond 0.05539 / 3.66 ( 1499) hydrogen bonds : angle 4.18320 / 2.94 ( 4070) metal coordination : bond 0.00477 / 0.32 ( 23) metal coordination : angle 3.36558 / 1.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.878 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: A 939 ASP cc_start: 0.4910 (m-30) cc_final: 0.4597 (p0) REVERT: A 1294 MET cc_start: 0.0717 (mtm) cc_final: 0.0481 (mtm) REVERT: A 1345 HIS cc_start: -0.1013 (t-90) cc_final: -0.1715 (m170) REVERT: B 38 HIS cc_start: 0.4178 (p-80) cc_final: 0.3669 (m90) REVERT: C 362 PHE cc_start: 0.6357 (t80) cc_final: 0.6068 (t80) REVERT: C 401 MET cc_start: 0.4025 (tpt) cc_final: 0.3808 (tpp) REVERT: a 120 MET cc_start: 0.8424 (mtm) cc_final: 0.8222 (mtm) REVERT: c 38 ASN cc_start: 0.8645 (m-40) cc_final: 0.8368 (m-40) REVERT: c 62 ILE cc_start: 0.8910 (tt) cc_final: 0.8420 (mt) REVERT: c 92 GLU cc_start: 0.6821 (pm20) cc_final: 0.6619 (pm20) REVERT: d 62 MET cc_start: 0.8598 (mmm) cc_final: 0.8193 (mmm) REVERT: e 120 MET cc_start: 0.8061 (mtp) cc_final: 0.7521 (tpp) REVERT: h 101 LEU cc_start: 0.8829 (mm) cc_final: 0.8622 (tp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1636 time to fit residues: 49.5364 Evaluate side-chains 136 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 180 optimal weight: 40.0000 chunk 119 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 271 optimal weight: 50.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS f 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.087127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.060992 restraints weight = 259631.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.062621 restraints weight = 149633.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.063706 restraints weight = 103690.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.064318 restraints weight = 81052.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.064841 restraints weight = 69720.685| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.205 29056 Z= 0.450 Angle : 0.660 23.097 40465 Z= 0.367 Chirality : 0.043 0.212 4466 Planarity : 0.004 0.075 4129 Dihedral : 26.359 87.012 6239 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2646 helix: 1.25 (0.13), residues: 1538 sheet: -0.48 (0.43), residues: 123 loop : -1.65 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 564 TYR 0.028 0.001 TYR E 489 PHE 0.022 0.001 PHE d 65 TRP 0.044 0.002 TRP D 236 HIS 0.009 0.001 HIS C 369 Details of bonding type rmsd/Z covalent geometry : bond 0.01026 / 0.45 (29033) covalent geometry : angle 0.65514 / 0.37 (40447) hydrogen bonds : bond 0.04488 / 2.95 ( 1499) hydrogen bonds : angle 3.96489 / 2.80 ( 4070) metal coordination : bond 0.00654 / 0.36 ( 23) metal coordination : angle 3.68389 / 1.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 ASP cc_start: 0.5046 (m-30) cc_final: 0.4711 (p0) REVERT: A 1151 TRP cc_start: 0.7042 (t-100) cc_final: 0.6839 (t-100) REVERT: A 1257 MET cc_start: 0.4542 (mtp) cc_final: 0.4278 (mtp) REVERT: A 1294 MET cc_start: 0.0528 (mtm) cc_final: 0.0308 (mtm) REVERT: B 38 HIS cc_start: 0.4358 (p-80) cc_final: 0.3954 (m170) REVERT: C 347 MET cc_start: -0.2376 (tpp) cc_final: -0.3004 (tmm) REVERT: C 401 MET cc_start: 0.4136 (tpt) cc_final: 0.3908 (tpp) REVERT: a 50 GLU cc_start: 0.8355 (tt0) cc_final: 0.8023 (pt0) REVERT: c 38 ASN cc_start: 0.8562 (m-40) cc_final: 0.8208 (m-40) REVERT: c 62 ILE cc_start: 0.8869 (tt) cc_final: 0.8410 (mt) REVERT: d 59 MET cc_start: 0.8898 (ptm) cc_final: 0.8663 (ptt) REVERT: d 62 MET cc_start: 0.8567 (mmm) cc_final: 0.8119 (mmm) REVERT: e 120 MET cc_start: 0.7994 (mtp) cc_final: 0.7472 (tpp) REVERT: h 101 LEU cc_start: 0.8888 (mm) cc_final: 0.8609 (tp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1741 time to fit residues: 53.4110 Evaluate side-chains 141 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 102 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 28 optimal weight: 0.0370 chunk 209 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A1137 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS f 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.092600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.064084 restraints weight = 248056.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.065843 restraints weight = 145051.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.066891 restraints weight = 102192.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.067153 restraints weight = 82014.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.067654 restraints weight = 72982.038| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.206 29056 Z= 0.454 Angle : 0.665 23.192 40465 Z= 0.370 Chirality : 0.042 0.211 4466 Planarity : 0.005 0.092 4129 Dihedral : 26.367 86.740 6239 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 1.34 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2646 helix: 1.22 (0.13), residues: 1550 sheet: -0.38 (0.45), residues: 122 loop : -1.55 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.023 0.001 TYR F 372 PHE 0.020 0.002 PHE h 65 TRP 0.044 0.002 TRP D 236 HIS 0.007 0.001 HIS F 346 Details of bonding type rmsd/Z covalent geometry : bond 0.01036 / 0.45 (29033) covalent geometry : angle 0.66136 / 0.37 (40447) hydrogen bonds : bond 0.04752 / 3.13 ( 1499) hydrogen bonds : angle 4.00958 / 2.83 ( 4070) metal coordination : bond 0.00439 / 0.24 ( 23) metal coordination : angle 3.20596 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 ASP cc_start: 0.5132 (m-30) cc_final: 0.4761 (p0) REVERT: A 1014 LEU cc_start: 0.7528 (mt) cc_final: 0.7241 (tp) REVERT: A 1257 MET cc_start: 0.4624 (mtp) cc_final: 0.4411 (mtp) REVERT: A 1294 MET cc_start: 0.0499 (mtm) cc_final: 0.0147 (ptp) REVERT: A 1345 HIS cc_start: -0.0878 (t-90) cc_final: -0.1586 (m170) REVERT: B 38 HIS cc_start: 0.4096 (p-80) cc_final: 0.3748 (m170) REVERT: B 239 ARG cc_start: 0.5123 (mtt180) cc_final: 0.4705 (mtt180) REVERT: C 347 MET cc_start: -0.2413 (tpp) cc_final: -0.2973 (tmm) REVERT: C 362 PHE cc_start: 0.5846 (t80) cc_final: 0.5542 (t80) REVERT: a 50 GLU cc_start: 0.8569 (tt0) cc_final: 0.8267 (tt0) REVERT: b 27 GLN cc_start: 0.7677 (pm20) cc_final: 0.7448 (pm20) REVERT: b 84 MET cc_start: 0.7489 (tpp) cc_final: 0.6458 (tpp) REVERT: b 85 ASP cc_start: 0.8427 (m-30) cc_final: 0.8099 (m-30) REVERT: c 38 ASN cc_start: 0.8593 (m-40) cc_final: 0.8193 (m-40) REVERT: c 62 ILE cc_start: 0.8993 (tt) cc_final: 0.8567 (mt) REVERT: d 59 MET cc_start: 0.9010 (ptm) cc_final: 0.8668 (ptt) REVERT: d 62 MET cc_start: 0.8766 (mmm) cc_final: 0.8364 (mmm) REVERT: e 120 MET cc_start: 0.8045 (mtp) cc_final: 0.7515 (tpp) REVERT: g 56 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8263 (mt-10) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1686 time to fit residues: 49.9539 Evaluate side-chains 142 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 2 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 GLN A1216 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS a 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.091313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.062778 restraints weight = 246519.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.064448 restraints weight = 144594.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.065535 restraints weight = 102825.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.066224 restraints weight = 82712.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.066478 restraints weight = 72296.164| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.205 29056 Z= 0.459 Angle : 0.696 23.386 40465 Z= 0.384 Chirality : 0.044 0.209 4466 Planarity : 0.005 0.057 4129 Dihedral : 26.497 87.360 6239 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2646 helix: 1.16 (0.13), residues: 1550 sheet: -0.42 (0.46), residues: 122 loop : -1.58 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 757 TYR 0.035 0.002 TYR g 50 PHE 0.033 0.002 PHE E 567 TRP 0.044 0.002 TRP D 236 HIS 0.013 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.46 (29033) covalent geometry : angle 0.69214 / 0.38 (40447) hydrogen bonds : bond 0.05260 / 3.50 ( 1499) hydrogen bonds : angle 4.06036 / 2.88 ( 4070) metal coordination : bond 0.00367 / 0.20 ( 23) metal coordination : angle 3.32522 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1014 LEU cc_start: 0.7532 (mt) cc_final: 0.7252 (tp) REVERT: A 1257 MET cc_start: 0.5042 (mtp) cc_final: 0.4694 (mtp) REVERT: A 1294 MET cc_start: 0.0479 (mtm) cc_final: 0.0117 (ptp) REVERT: A 1345 HIS cc_start: -0.0770 (t-90) cc_final: -0.1538 (m170) REVERT: E 442 TYR cc_start: 0.2644 (m-10) cc_final: 0.2300 (m-80) REVERT: B 204 MET cc_start: 0.0015 (mtp) cc_final: -0.0241 (ptp) REVERT: C 347 MET cc_start: -0.2540 (tpp) cc_final: -0.3133 (tmm) REVERT: C 362 PHE cc_start: 0.5970 (t80) cc_final: 0.5564 (t80) REVERT: a 50 GLU cc_start: 0.8590 (tt0) cc_final: 0.8198 (tt0) REVERT: b 27 GLN cc_start: 0.7522 (pm20) cc_final: 0.7027 (pm20) REVERT: b 81 VAL cc_start: 0.6272 (t) cc_final: 0.6025 (t) REVERT: b 85 ASP cc_start: 0.8485 (m-30) cc_final: 0.8142 (p0) REVERT: c 38 ASN cc_start: 0.8682 (m-40) cc_final: 0.8408 (m110) REVERT: c 39 TYR cc_start: 0.8839 (m-80) cc_final: 0.8319 (m-80) REVERT: c 62 ILE cc_start: 0.9059 (tt) cc_final: 0.8807 (mm) REVERT: d 62 MET cc_start: 0.8747 (mmm) cc_final: 0.8418 (mmm) REVERT: e 120 MET cc_start: 0.8055 (mtp) cc_final: 0.7499 (tpp) REVERT: g 56 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8356 (mt-10) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1635 time to fit residues: 47.8361 Evaluate side-chains 133 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 218 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 126 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 270 optimal weight: 50.0000 chunk 200 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS F 346 HIS f 93 GLN h 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.090673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.062217 restraints weight = 249456.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.063866 restraints weight = 146298.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.064971 restraints weight = 103375.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.065553 restraints weight = 82797.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.066053 restraints weight = 73024.446| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.462 Angle : 0.700 23.454 40465 Z= 0.386 Chirality : 0.044 0.213 4466 Planarity : 0.005 0.049 4129 Dihedral : 26.562 87.749 6239 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.04 % Allowed : 1.34 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2646 helix: 1.13 (0.13), residues: 1543 sheet: -0.47 (0.47), residues: 120 loop : -1.59 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 384 TYR 0.026 0.002 TYR F 372 PHE 0.027 0.002 PHE E 567 TRP 0.044 0.002 TRP D 236 HIS 0.014 0.002 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01052 / 0.46 (29033) covalent geometry : angle 0.69707 / 0.39 (40447) hydrogen bonds : bond 0.05376 / 3.58 ( 1499) hydrogen bonds : angle 4.09366 / 2.89 ( 4070) metal coordination : bond 0.00909 / 0.58 ( 23) metal coordination : angle 3.28983 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 ASP cc_start: 0.5289 (m-30) cc_final: 0.4491 (p0) REVERT: A 1014 LEU cc_start: 0.7530 (mt) cc_final: 0.7253 (tp) REVERT: A 1294 MET cc_start: 0.0490 (mtm) cc_final: 0.0096 (ptp) REVERT: A 1345 HIS cc_start: -0.0446 (t-90) cc_final: -0.1274 (m170) REVERT: E 437 ILE cc_start: 0.4804 (mm) cc_final: 0.4569 (mm) REVERT: E 442 TYR cc_start: 0.2712 (m-10) cc_final: 0.2462 (m-80) REVERT: B 247 TYR cc_start: 0.8073 (t80) cc_final: 0.7624 (t80) REVERT: C 362 PHE cc_start: 0.5937 (t80) cc_final: 0.5568 (t80) REVERT: b 81 VAL cc_start: 0.6333 (t) cc_final: 0.6116 (t) REVERT: b 85 ASP cc_start: 0.8605 (m-30) cc_final: 0.8103 (p0) REVERT: c 38 ASN cc_start: 0.8770 (m-40) cc_final: 0.8363 (m110) REVERT: c 62 ILE cc_start: 0.9061 (tt) cc_final: 0.8848 (mm) REVERT: d 62 MET cc_start: 0.8788 (mmm) cc_final: 0.8570 (mmm) REVERT: e 120 MET cc_start: 0.8024 (mtp) cc_final: 0.7512 (tpp) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1681 time to fit residues: 45.8342 Evaluate side-chains 135 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 83 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 186 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 193 optimal weight: 0.4980 chunk 284 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 358 GLN F 346 HIS ** c 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.090188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.062361 restraints weight = 248349.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.064013 restraints weight = 145356.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.065048 restraints weight = 102386.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.065278 restraints weight = 82005.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.065912 restraints weight = 73860.555| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29056 Z= 0.450 Angle : 0.659 23.429 40465 Z= 0.368 Chirality : 0.043 0.202 4466 Planarity : 0.004 0.060 4129 Dihedral : 26.466 88.492 6239 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2646 helix: 1.30 (0.13), residues: 1546 sheet: -0.51 (0.46), residues: 123 loop : -1.48 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1009 TYR 0.025 0.001 TYR F 372 PHE 0.027 0.001 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.007 0.001 HIS F 346 Details of bonding type rmsd/Z covalent geometry : bond 0.01027 / 0.45 (29033) covalent geometry : angle 0.65683 / 0.37 (40447) hydrogen bonds : bond 0.04534 / 2.97 ( 1499) hydrogen bonds : angle 3.93611 / 2.78 ( 4070) metal coordination : bond 0.00329 / 0.18 ( 23) metal coordination : angle 2.84841 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1014 LEU cc_start: 0.7570 (mt) cc_final: 0.7243 (tp) REVERT: A 1164 MET cc_start: 0.5058 (mtt) cc_final: 0.4773 (mtm) REVERT: A 1294 MET cc_start: 0.0796 (mtm) cc_final: 0.0487 (ptp) REVERT: A 1345 HIS cc_start: -0.0497 (t-90) cc_final: -0.1363 (m170) REVERT: E 437 ILE cc_start: 0.5146 (mm) cc_final: 0.4727 (mm) REVERT: B 128 MET cc_start: 0.7480 (ptt) cc_final: 0.7253 (ptt) REVERT: B 247 TYR cc_start: 0.8054 (t80) cc_final: 0.7696 (t80) REVERT: C 347 MET cc_start: -0.3925 (tpt) cc_final: -0.4253 (tmm) REVERT: C 362 PHE cc_start: 0.6049 (t80) cc_final: 0.5760 (t80) REVERT: F 560 MET cc_start: 0.2496 (tpt) cc_final: 0.2227 (ttp) REVERT: b 81 VAL cc_start: 0.6468 (t) cc_final: 0.6212 (t) REVERT: b 85 ASP cc_start: 0.8589 (m-30) cc_final: 0.8140 (p0) REVERT: c 38 ASN cc_start: 0.8755 (m-40) cc_final: 0.8455 (m110) REVERT: c 39 TYR cc_start: 0.8812 (m-80) cc_final: 0.8146 (m-80) REVERT: c 62 ILE cc_start: 0.9024 (tt) cc_final: 0.8794 (mm) REVERT: d 62 MET cc_start: 0.8886 (mmm) cc_final: 0.8619 (mmm) REVERT: h 62 MET cc_start: 0.8560 (mmm) cc_final: 0.8099 (mmm) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1632 time to fit residues: 47.7970 Evaluate side-chains 135 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 116 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN E 267 ASN E 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS a 125 GLN f 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.090521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.062025 restraints weight = 245443.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.063555 restraints weight = 149062.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.064470 restraints weight = 108479.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.064692 restraints weight = 88994.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.065388 restraints weight = 81239.470| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.478 Angle : 0.796 23.772 40465 Z= 0.432 Chirality : 0.047 0.237 4466 Planarity : 0.006 0.052 4129 Dihedral : 26.765 89.984 6239 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 0.08 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2646 helix: 0.79 (0.13), residues: 1546 sheet: -0.75 (0.46), residues: 117 loop : -1.67 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG a 49 TYR 0.027 0.002 TYR F 372 PHE 0.037 0.003 PHE E 552 TRP 0.044 0.003 TRP D 236 HIS 0.014 0.002 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01085 / 0.48 (29033) covalent geometry : angle 0.79221 / 0.43 (40447) hydrogen bonds : bond 0.07372 / 4.93 ( 1499) hydrogen bonds : angle 4.36596 / 3.08 ( 4070) metal coordination : bond 0.00459 / 0.26 ( 23) metal coordination : angle 3.75490 / 1.78 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1014 LEU cc_start: 0.7493 (mt) cc_final: 0.7221 (tp) REVERT: A 1164 MET cc_start: 0.5099 (mtt) cc_final: 0.4879 (mtm) REVERT: A 1257 MET cc_start: 0.5814 (mtt) cc_final: 0.5530 (mtt) REVERT: A 1294 MET cc_start: 0.0613 (mtm) cc_final: 0.0242 (ptp) REVERT: A 1345 HIS cc_start: -0.0063 (t-90) cc_final: -0.0878 (m170) REVERT: E 387 PHE cc_start: 0.2033 (p90) cc_final: 0.1533 (t80) REVERT: E 395 ILE cc_start: 0.2853 (pt) cc_final: 0.2578 (pt) REVERT: B 247 TYR cc_start: 0.8351 (t80) cc_final: 0.7931 (t80) REVERT: C 347 MET cc_start: -0.3905 (tpt) cc_final: -0.4393 (tmm) REVERT: F 560 MET cc_start: 0.2864 (tpt) cc_final: 0.2607 (ttp) REVERT: b 59 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8389 (pttm) REVERT: b 85 ASP cc_start: 0.8528 (m-30) cc_final: 0.8304 (p0) REVERT: c 38 ASN cc_start: 0.8743 (m-40) cc_final: 0.8472 (m110) REVERT: e 120 MET cc_start: 0.7686 (mtp) cc_final: 0.6967 (tpp) REVERT: g 56 GLU cc_start: 0.9025 (mp0) cc_final: 0.8774 (mp0) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.1757 time to fit residues: 47.3068 Evaluate side-chains 128 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 229 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 180 optimal weight: 50.0000 chunk 182 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN E 302 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN C 350 GLN F 346 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.088866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.061305 restraints weight = 251473.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.062916 restraints weight = 148524.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.063933 restraints weight = 105266.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.064586 restraints weight = 84330.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.064980 restraints weight = 73492.919| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29056 Z= 0.452 Angle : 0.683 23.667 40465 Z= 0.380 Chirality : 0.044 0.208 4466 Planarity : 0.004 0.061 4129 Dihedral : 26.701 89.609 6239 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2646 helix: 1.06 (0.13), residues: 1532 sheet: -0.49 (0.50), residues: 106 loop : -1.54 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 72 TYR 0.026 0.001 TYR F 372 PHE 0.025 0.002 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01031 / 0.45 (29033) covalent geometry : angle 0.68013 / 0.38 (40447) hydrogen bonds : bond 0.04924 / 3.25 ( 1499) hydrogen bonds : angle 4.11772 / 2.90 ( 4070) metal coordination : bond 0.00421 / 0.23 ( 23) metal coordination : angle 3.12754 / 1.46 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9033.95 seconds wall clock time: 154 minutes 48.97 seconds (9288.97 seconds total)