Starting phenix.real_space_refine on Sun Jul 5 10:44:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9f_37367/07_2026/8w9f_37367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9f_37367/07_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_37367/07_2026/8w9f_37367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9f_37367/07_2026/8w9f_37367_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9f_37367/07_2026/8w9f_37367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9f_37367/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.63, per 1000 atoms: 0.20 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: 2.27 Conformation dependent library (CDL) restraints added in 920.8 milliseconds 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: 3.46 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: 8.22 Time building geometry restraints manager: 3.08 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.030 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- 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 : 1.142 53.767 40465 Z= 0.755 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 1.03847 / 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 : 0.946 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: A 778 LEU cc_start: 0.6060 (mm) cc_final: 0.5119 (mm) REVERT: A 903 GLU cc_start: 0.1730 (OUTLIER) cc_final: 0.0965 (mt-10) REVERT: A 1065 LEU cc_start: -0.4742 (OUTLIER) cc_final: -0.5547 (mp) REVERT: A 1332 ASP cc_start: 0.0726 (t0) cc_final: 0.0448 (m-30) REVERT: A 1345 HIS cc_start: -0.1068 (t-90) cc_final: -0.1314 (m170) REVERT: E 108 VAL cc_start: 0.2626 (OUTLIER) cc_final: 0.2260 (m) REVERT: E 123 ILE cc_start: -0.1158 (OUTLIER) cc_final: -0.1537 (mm) REVERT: E 272 PHE cc_start: 0.2359 (OUTLIER) cc_final: 0.2004 (p90) REVERT: E 387 PHE cc_start: 0.1003 (OUTLIER) cc_final: 0.0553 (p90) REVERT: E 388 ASN cc_start: 0.2422 (OUTLIER) cc_final: 0.1934 (t0) REVERT: B 2 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.3199 (t) REVERT: B 14 LYS cc_start: -0.0227 (OUTLIER) cc_final: -0.1075 (mtpt) REVERT: B 32 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.0788 (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: 0.3359 (p0) REVERT: B 111 PRO cc_start: -0.0664 (OUTLIER) cc_final: -0.0940 (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: 0.4336 (p) REVERT: B 204 MET cc_start: 0.3062 (ttt) cc_final: 0.2678 (ttm) REVERT: C 222 LEU cc_start: 0.0502 (OUTLIER) cc_final: 0.0091 (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: -0.1226 (mttt) REVERT: C 376 ASP cc_start: -0.1499 (OUTLIER) cc_final: -0.2452 (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: F 369 ARG cc_start: 0.0844 (ptm160) cc_final: 0.0644 (tpt90) REVERT: a 86 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7961 (t) REVERT: a 89 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8596 (m) REVERT: b 58 LEU cc_start: 0.8296 (tp) cc_final: 0.8078 (tt) REVERT: b 88 TYR cc_start: 0.6500 (m-10) cc_final: 0.6236 (m-10) REVERT: c 30 VAL cc_start: 0.8496 (t) cc_final: 0.8223 (p) REVERT: c 62 ILE cc_start: 0.8790 (tt) cc_final: 0.8214 (mt) REVERT: c 90 ASP cc_start: 0.7134 (t0) cc_final: 0.6908 (t0) REVERT: c 107 VAL cc_start: 0.8332 (m) cc_final: 0.8051 (t) REVERT: d 79 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7804 (mmm160) REVERT: e 60 LEU cc_start: 0.8374 (mt) cc_final: 0.8172 (mm) REVERT: e 87 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8399 (t) REVERT: f 84 MET cc_start: 0.7618 (mmm) cc_final: 0.6637 (tpp) REVERT: h 83 TYR cc_start: 0.7780 (m-10) cc_final: 0.7357 (m-10) REVERT: h 101 LEU cc_start: 0.8847 (mt) cc_final: 0.8410 (tp) outliers start: 180 outliers final: 25 residues processed: 607 average time/residue: 0.2080 time to fit residues: 192.2034 Evaluate side-chains 232 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 267 ASN 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** 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 39 HIS e 125 GLN f 25 ASN f 93 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.097312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.067762 restraints weight = 243747.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.069584 restraints weight = 143127.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.070673 restraints weight = 101252.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.071420 restraints weight = 81759.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.071877 restraints weight = 71532.220| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29056 Z= 0.471 Angle : 0.794 22.810 40465 Z= 0.440 Chirality : 0.047 0.280 4466 Planarity : 0.006 0.111 4129 Dihedral : 26.533 89.387 6239 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.20 % Favored : 95.50 % Rotamer: Outliers : 0.46 % Allowed : 3.59 % Favored : 95.95 % 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: -0.65 (0.16), residues: 2646 helix: 0.63 (0.13), residues: 1533 sheet: -0.62 (0.45), residues: 118 loop : -2.13 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 182 TYR 0.053 0.002 TYR E 514 PHE 0.025 0.002 PHE g 25 TRP 0.044 0.003 TRP D 236 HIS 0.019 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01067 / 0.47 (29033) covalent geometry : angle 0.78499 / 0.44 (40447) hydrogen bonds : bond 0.06006 / 3.89 ( 1499) hydrogen bonds : angle 4.45388 / 3.10 ( 4070) metal coordination : bond 0.01788 / 1.08 ( 23) metal coordination : angle 5.80232 / 3.07 ( 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 269 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 706 VAL cc_start: 0.5907 (t) cc_final: 0.5607 (m) REVERT: A 939 ASP cc_start: 0.4631 (m-30) cc_final: 0.4314 (p0) REVERT: A 948 LEU cc_start: 0.6573 (mp) cc_final: 0.6259 (mm) REVERT: A 1257 MET cc_start: 0.6131 (mtt) cc_final: 0.5156 (mpp) REVERT: A 1294 MET cc_start: 0.1718 (mtm) cc_final: 0.0836 (mtt) REVERT: A 1345 HIS cc_start: -0.0913 (t-90) cc_final: -0.1562 (m170) REVERT: E 331 ASN cc_start: 0.5042 (t0) cc_final: 0.4206 (p0) REVERT: E 428 TRP cc_start: 0.1407 (m100) cc_final: 0.1160 (m100) REVERT: B 38 HIS cc_start: 0.4337 (p-80) cc_final: 0.3909 (m170) REVERT: B 247 TYR cc_start: 0.8114 (t80) cc_final: 0.7819 (t80) REVERT: D 387 TYR cc_start: -0.0954 (m-80) cc_final: -0.1311 (m-10) REVERT: F 257 PHE cc_start: -0.0866 (m-10) cc_final: -0.1114 (m-80) REVERT: a 134 ARG cc_start: 0.6813 (mmm-85) cc_final: 0.6478 (ptt180) REVERT: b 84 MET cc_start: 0.7232 (tpp) cc_final: 0.6709 (tpp) REVERT: b 85 ASP cc_start: 0.8008 (m-30) cc_final: 0.7759 (m-30) REVERT: b 88 TYR cc_start: 0.6710 (m-10) cc_final: 0.6040 (m-10) REVERT: c 38 ASN cc_start: 0.8645 (m110) cc_final: 0.8268 (m-40) REVERT: c 62 ILE cc_start: 0.8942 (tt) cc_final: 0.8555 (mt) REVERT: c 90 ASP cc_start: 0.7580 (t0) cc_final: 0.7037 (t0) REVERT: e 60 LEU cc_start: 0.8062 (mt) cc_final: 0.7601 (pp) REVERT: f 35 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8197 (mtp85) REVERT: f 84 MET cc_start: 0.6913 (mmm) cc_final: 0.6531 (tpp) REVERT: h 45 LEU cc_start: 0.7652 (pp) cc_final: 0.7408 (tp) outliers start: 11 outliers final: 4 residues processed: 268 average time/residue: 0.1887 time to fit residues: 78.7561 Evaluate side-chains 165 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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: 10.0000 chunk 200 optimal weight: 0.1980 chunk 173 optimal weight: 50.0000 chunk 232 optimal weight: 0.9980 chunk 271 optimal weight: 40.0000 chunk 87 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 169 optimal weight: 0.0070 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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** A 921 GLN ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN E 521 GLN B 135 ASN ** 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** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS d 82 HIS f 75 HIS f 93 GLN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.088780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.062836 restraints weight = 257033.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.064619 restraints weight = 145293.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.065355 restraints weight = 98752.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.066288 restraints weight = 79895.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.066797 restraints weight = 67345.212| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3567 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= 0.455 Angle : 0.692 22.882 40465 Z= 0.385 Chirality : 0.043 0.339 4466 Planarity : 0.005 0.100 4129 Dihedral : 26.379 88.871 6239 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.80 % Rotamer: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % 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: -0.09 (0.16), residues: 2646 helix: 1.10 (0.13), residues: 1525 sheet: -0.46 (0.45), residues: 117 loop : -1.86 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 92 TYR 0.024 0.002 TYR E 514 PHE 0.027 0.002 PHE B 284 TRP 0.043 0.002 TRP D 236 HIS 0.011 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.46 (29033) covalent geometry : angle 0.68626 / 0.38 (40447) hydrogen bonds : bond 0.04953 / 3.23 ( 1499) hydrogen bonds : angle 4.13474 / 2.89 ( 4070) metal coordination : bond 0.00890 / 0.63 ( 23) metal coordination : angle 4.36662 / 2.39 ( 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 221 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.3717 (mtt) cc_final: 0.3498 (mtm) REVERT: A 948 LEU cc_start: 0.6441 (mp) cc_final: 0.6204 (mm) REVERT: A 1257 MET cc_start: 0.6038 (mtt) cc_final: 0.5061 (mpp) REVERT: B 38 HIS cc_start: 0.4301 (p-80) cc_final: 0.3972 (m170) REVERT: B 45 ILE cc_start: 0.5774 (mt) cc_final: 0.5435 (tt) REVERT: B 47 MET cc_start: 0.4615 (tpp) cc_final: 0.3274 (mtp) REVERT: a 120 MET cc_start: 0.8063 (mtm) cc_final: 0.7435 (ptp) REVERT: a 126 LEU cc_start: 0.8176 (tp) cc_final: 0.7918 (tp) REVERT: a 134 ARG cc_start: 0.6782 (mmm-85) cc_final: 0.6486 (ptt180) REVERT: c 38 ASN cc_start: 0.8518 (m110) cc_final: 0.8183 (m-40) REVERT: e 60 LEU cc_start: 0.7868 (mt) cc_final: 0.7401 (pp) REVERT: f 84 MET cc_start: 0.6643 (mmm) cc_final: 0.6388 (tpp) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1757 time to fit residues: 63.1602 Evaluate side-chains 149 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 5.9990 chunk 233 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 248 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 A1137 ASN A1234 ASN E 346 HIS E 347 ASN E 350 GLN E 352 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** E 510 GLN ** 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 330 HIS ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS c 84 GLN f 93 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.086552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.060618 restraints weight = 257699.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.062241 restraints weight = 145923.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.063314 restraints weight = 100137.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.063957 restraints weight = 78037.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.064411 restraints weight = 67022.823| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29056 Z= 0.465 Angle : 0.725 23.363 40465 Z= 0.401 Chirality : 0.044 0.251 4466 Planarity : 0.005 0.088 4129 Dihedral : 26.529 86.117 6239 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.31 % Rotamer: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % 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: -0.06 (0.16), residues: 2646 helix: 1.06 (0.13), residues: 1533 sheet: -0.69 (0.43), residues: 123 loop : -1.73 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 384 TYR 0.025 0.002 TYR F 372 PHE 0.029 0.002 PHE d 65 TRP 0.044 0.002 TRP D 236 HIS 0.020 0.002 HIS C 369 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.47 (29033) covalent geometry : angle 0.72155 / 0.40 (40447) hydrogen bonds : bond 0.05918 / 3.91 ( 1499) hydrogen bonds : angle 4.16958 / 2.93 ( 4070) metal coordination : bond 0.00550 / 0.37 ( 23) metal coordination : angle 3.39948 / 1.71 ( 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 186 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6557 (mp) cc_final: 0.6226 (mm) REVERT: A 1345 HIS cc_start: -0.1021 (t-90) cc_final: -0.1719 (m170) REVERT: E 507 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6853 (tp30) REVERT: B 38 HIS cc_start: 0.4304 (p-80) cc_final: 0.3802 (m170) REVERT: B 45 ILE cc_start: 0.5662 (mt) cc_final: 0.5318 (tt) REVERT: B 47 MET cc_start: 0.4231 (tpp) cc_final: 0.3340 (mtp) REVERT: C 362 PHE cc_start: 0.5846 (t80) cc_final: 0.5550 (t80) REVERT: a 120 MET cc_start: 0.8381 (mtm) cc_final: 0.8027 (mtm) REVERT: c 38 ASN cc_start: 0.8647 (m110) cc_final: 0.8281 (m110) REVERT: c 90 ASP cc_start: 0.6864 (t0) cc_final: 0.6498 (t0) REVERT: e 60 LEU cc_start: 0.7815 (mt) cc_final: 0.7267 (pp) REVERT: e 105 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8108 (tm-30) REVERT: e 120 MET cc_start: 0.8029 (mtp) cc_final: 0.7545 (tpp) REVERT: h 101 LEU cc_start: 0.8914 (mt) cc_final: 0.8531 (tp) REVERT: G 22 MET cc_start: 0.0930 (mmm) cc_final: 0.0722 (mmm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1827 time to fit residues: 55.4869 Evaluate side-chains 137 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 180 optimal weight: 50.0000 chunk 119 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 271 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** 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 329 GLN F 346 HIS c 38 ASN f 93 GLN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.086996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.060885 restraints weight = 259857.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.062634 restraints weight = 146089.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.063579 restraints weight = 99572.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.064444 restraints weight = 78909.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.064846 restraints weight = 66747.556| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4543 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= 0.452 Angle : 0.660 23.128 40465 Z= 0.370 Chirality : 0.043 0.195 4466 Planarity : 0.004 0.078 4129 Dihedral : 26.490 86.619 6239 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % 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: 0.17 (0.16), residues: 2646 helix: 1.22 (0.13), residues: 1531 sheet: -0.38 (0.45), residues: 123 loop : -1.61 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 40 TYR 0.026 0.001 TYR E 489 PHE 0.032 0.002 PHE F 326 TRP 0.043 0.002 TRP D 236 HIS 0.006 0.001 HIS F 346 Details of bonding type rmsd/Z covalent geometry : bond 0.01031 / 0.45 (29033) covalent geometry : angle 0.65541 / 0.37 (40447) hydrogen bonds : bond 0.04631 / 3.04 ( 1499) hydrogen bonds : angle 4.03292 / 2.85 ( 4070) metal coordination : bond 0.00411 / 0.27 ( 23) metal coordination : angle 3.79287 / 1.86 ( 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 186 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6528 (mp) cc_final: 0.6264 (mm) REVERT: B 38 HIS cc_start: 0.4320 (p-80) cc_final: 0.3768 (m170) REVERT: C 362 PHE cc_start: 0.5950 (t80) cc_final: 0.5671 (t80) REVERT: b 84 MET cc_start: 0.7363 (tpp) cc_final: 0.5937 (tpp) REVERT: b 85 ASP cc_start: 0.8162 (m-30) cc_final: 0.7869 (m-30) REVERT: b 88 TYR cc_start: 0.7069 (m-10) cc_final: 0.6834 (m-10) REVERT: c 38 ASN cc_start: 0.8625 (m-40) cc_final: 0.8240 (m110) REVERT: c 62 ILE cc_start: 0.8818 (tt) cc_final: 0.8504 (mm) REVERT: d 59 MET cc_start: 0.8889 (ptm) cc_final: 0.8688 (ptt) REVERT: d 62 MET cc_start: 0.8513 (mmm) cc_final: 0.8151 (mmm) REVERT: e 60 LEU cc_start: 0.7925 (mt) cc_final: 0.7289 (pp) REVERT: e 105 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7870 (tm-30) REVERT: e 120 MET cc_start: 0.7970 (mtp) cc_final: 0.7444 (tpp) REVERT: h 101 LEU cc_start: 0.8881 (mt) cc_final: 0.8535 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1768 time to fit residues: 54.2617 Evaluate side-chains 139 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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: 8.9990 chunk 226 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 284 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** A1216 ASN E 406 HIS E 495 GLN ** E 510 GLN ** 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** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN F 330 ASN F 346 HIS ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.091066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.062741 restraints weight = 250786.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.064427 restraints weight = 146372.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.065425 restraints weight = 103645.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.065702 restraints weight = 83639.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.066527 restraints weight = 73868.555| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.207 29056 Z= 0.473 Angle : 0.754 23.359 40465 Z= 0.414 Chirality : 0.045 0.216 4466 Planarity : 0.005 0.068 4129 Dihedral : 26.719 87.887 6239 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % 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: -0.20 (0.16), residues: 2646 helix: 0.81 (0.13), residues: 1550 sheet: -0.26 (0.47), residues: 120 loop : -1.64 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 384 TYR 0.029 0.002 TYR B 346 PHE 0.030 0.002 PHE d 65 TRP 0.045 0.002 TRP D 236 HIS 0.010 0.002 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.47 (29033) covalent geometry : angle 0.75033 / 0.41 (40447) hydrogen bonds : bond 0.06522 / 4.34 ( 1499) hydrogen bonds : angle 4.27011 / 3.02 ( 4070) metal coordination : bond 0.00456 / 0.26 ( 23) metal coordination : angle 3.74035 / 1.75 ( 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 173 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6591 (mp) cc_final: 0.6281 (mm) REVERT: A 1014 LEU cc_start: 0.7616 (mt) cc_final: 0.7306 (tp) REVERT: A 1294 MET cc_start: 0.0583 (mtm) cc_final: 0.0251 (ptp) REVERT: A 1345 HIS cc_start: -0.0935 (t-90) cc_final: -0.1714 (m170) REVERT: C 347 MET cc_start: -0.3858 (tpt) cc_final: -0.4362 (tmm) REVERT: C 362 PHE cc_start: 0.6050 (t80) cc_final: 0.5727 (t80) REVERT: F 329 GLN cc_start: 0.5556 (pt0) cc_final: 0.4901 (mm110) REVERT: a 50 GLU cc_start: 0.8254 (tt0) cc_final: 0.7884 (pt0) REVERT: a 120 MET cc_start: 0.8513 (mtm) cc_final: 0.8131 (mtm) REVERT: b 85 ASP cc_start: 0.8579 (m-30) cc_final: 0.8309 (m-30) REVERT: c 38 ASN cc_start: 0.8844 (m-40) cc_final: 0.8470 (m110) REVERT: c 62 ILE cc_start: 0.9022 (tt) cc_final: 0.8704 (mm) REVERT: d 62 MET cc_start: 0.8722 (mmm) cc_final: 0.8433 (mmm) REVERT: e 60 LEU cc_start: 0.7910 (mt) cc_final: 0.7285 (pp) REVERT: h 101 LEU cc_start: 0.8922 (mt) cc_final: 0.8636 (tp) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1488 time to fit residues: 43.0718 Evaluate side-chains 138 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 9.9990 chunk 283 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 A1163 GLN ** E 495 GLN ** 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 369 HIS F 346 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 = 0.4291 r_free = 0.4291 target = 0.091288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.062907 restraints weight = 247621.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.064539 restraints weight = 143840.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.065615 restraints weight = 101662.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.065866 restraints weight = 81531.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.066477 restraints weight = 72245.037| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.5611 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 : 0.689 23.413 40465 Z= 0.384 Chirality : 0.044 0.204 4466 Planarity : 0.005 0.057 4129 Dihedral : 26.751 87.954 6239 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 1.63 % Favored : 98.33 % 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: 0.01 (0.16), residues: 2646 helix: 1.02 (0.13), residues: 1551 sheet: -0.39 (0.47), residues: 123 loop : -1.59 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 757 TYR 0.029 0.002 TYR g 50 PHE 0.032 0.002 PHE d 65 TRP 0.044 0.002 TRP D 236 HIS 0.007 0.001 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.46 (29033) covalent geometry : angle 0.68553 / 0.38 (40447) hydrogen bonds : bond 0.04936 / 3.26 ( 1499) hydrogen bonds : angle 4.11768 / 2.92 ( 4070) metal coordination : bond 0.00373 / 0.21 ( 23) metal coordination : angle 3.30396 / 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 169 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6629 (mp) cc_final: 0.6379 (mm) REVERT: A 1014 LEU cc_start: 0.7592 (mt) cc_final: 0.7294 (tp) REVERT: A 1294 MET cc_start: 0.0459 (mtm) cc_final: -0.0045 (ptp) REVERT: A 1301 PHE cc_start: 0.5486 (m-80) cc_final: 0.4126 (m-80) REVERT: A 1345 HIS cc_start: -0.0685 (t-90) cc_final: -0.1516 (m170) REVERT: B 204 MET cc_start: 0.0117 (mtp) cc_final: -0.0283 (ptp) REVERT: B 247 TYR cc_start: 0.8097 (t80) cc_final: 0.7769 (t80) REVERT: C 347 MET cc_start: -0.3768 (tpt) cc_final: -0.4157 (tmm) REVERT: C 362 PHE cc_start: 0.5941 (t80) cc_final: 0.5574 (t80) REVERT: F 329 GLN cc_start: 0.5220 (pt0) cc_final: 0.4435 (mm-40) REVERT: b 85 ASP cc_start: 0.8581 (m-30) cc_final: 0.8370 (m-30) REVERT: c 38 ASN cc_start: 0.8823 (m-40) cc_final: 0.8527 (m110) REVERT: c 62 ILE cc_start: 0.8998 (tt) cc_final: 0.8707 (mm) REVERT: e 60 LEU cc_start: 0.7782 (mt) cc_final: 0.7185 (pp) REVERT: g 56 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8236 (mm-30) REVERT: h 101 LEU cc_start: 0.8926 (mt) cc_final: 0.8679 (tp) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1646 time to fit residues: 47.4129 Evaluate side-chains 138 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 40.0000 chunk 126 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 270 optimal weight: 50.0000 chunk 200 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** E 495 GLN ** 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 F 346 HIS ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.091206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.062811 restraints weight = 249266.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.064512 restraints weight = 144421.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.065563 restraints weight = 101655.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.065787 restraints weight = 81990.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.066516 restraints weight = 74297.566| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.5789 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= 0.452 Angle : 0.668 23.445 40465 Z= 0.372 Chirality : 0.043 0.205 4466 Planarity : 0.004 0.056 4129 Dihedral : 26.666 87.512 6239 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 0.04 % Allowed : 0.58 % Favored : 99.37 % 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: 0.14 (0.16), residues: 2646 helix: 1.15 (0.13), residues: 1548 sheet: -0.39 (0.48), residues: 122 loop : -1.58 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 384 TYR 0.025 0.002 TYR F 372 PHE 0.028 0.002 PHE d 65 TRP 0.043 0.002 TRP D 236 HIS 0.011 0.001 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.45 (29033) covalent geometry : angle 0.66497 / 0.37 (40447) hydrogen bonds : bond 0.04887 / 3.23 ( 1499) hydrogen bonds : angle 4.03664 / 2.87 ( 4070) metal coordination : bond 0.00410 / 0.26 ( 23) metal coordination : angle 3.08026 / 1.45 ( 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 178 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6627 (mp) cc_final: 0.6300 (mm) REVERT: A 1014 LEU cc_start: 0.7626 (mt) cc_final: 0.7325 (tp) REVERT: A 1071 ARG cc_start: 0.3511 (mpp-170) cc_final: 0.2709 (tpt170) REVERT: A 1294 MET cc_start: 0.0560 (mtm) cc_final: 0.0182 (ptp) REVERT: A 1345 HIS cc_start: -0.0471 (t-90) cc_final: -0.1314 (m170) REVERT: B 61 MET cc_start: -0.1646 (ptm) cc_final: -0.1859 (ptm) REVERT: B 247 TYR cc_start: 0.8053 (t80) cc_final: 0.7711 (t80) REVERT: B 313 TYR cc_start: 0.4364 (m-80) cc_final: 0.4155 (m-80) REVERT: C 347 MET cc_start: -0.4003 (tpt) cc_final: -0.4494 (tmm) REVERT: C 362 PHE cc_start: 0.5986 (t80) cc_final: 0.5631 (t80) REVERT: F 560 MET cc_start: 0.2410 (tpt) cc_final: 0.2167 (ttp) REVERT: b 59 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8341 (pttm) REVERT: b 74 GLU cc_start: 0.7424 (pp20) cc_final: 0.7197 (pt0) REVERT: b 81 VAL cc_start: 0.6324 (t) cc_final: 0.6085 (t) REVERT: b 85 ASP cc_start: 0.8653 (m-30) cc_final: 0.8129 (p0) REVERT: c 38 ASN cc_start: 0.8724 (m-40) cc_final: 0.8288 (m110) REVERT: c 62 ILE cc_start: 0.9006 (tt) cc_final: 0.8681 (mm) REVERT: d 62 MET cc_start: 0.8742 (mmm) cc_final: 0.8490 (mmm) REVERT: e 60 LEU cc_start: 0.7757 (mt) cc_final: 0.7218 (pp) REVERT: g 56 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8347 (mp0) REVERT: h 101 LEU cc_start: 0.8924 (mt) cc_final: 0.8694 (tp) REVERT: G 22 MET cc_start: 0.2074 (mmm) cc_final: 0.1793 (mtp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1689 time to fit residues: 49.7709 Evaluate side-chains 139 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 20.0000 chunk 110 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 186 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 205 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** A1004 ASN E 393 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** 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** F 346 HIS a 113 HIS b 27 GLN h 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.090164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.062031 restraints weight = 247835.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.063646 restraints weight = 145428.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.064657 restraints weight = 103860.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.064912 restraints weight = 83876.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.065687 restraints weight = 73281.462| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.6179 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= 0.460 Angle : 0.699 23.650 40465 Z= 0.389 Chirality : 0.044 0.207 4466 Planarity : 0.005 0.074 4129 Dihedral : 26.720 88.955 6239 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 0.50 % Favored : 99.42 % 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: 0.02 (0.16), residues: 2646 helix: 1.05 (0.13), residues: 1552 sheet: -0.59 (0.47), residues: 115 loop : -1.62 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 384 TYR 0.031 0.002 TYR B 232 PHE 0.064 0.002 PHE E 387 TRP 0.069 0.003 TRP E 187 HIS 0.009 0.002 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01050 / 0.46 (29033) covalent geometry : angle 0.69629 / 0.39 (40447) hydrogen bonds : bond 0.05413 / 3.59 ( 1499) hydrogen bonds : angle 4.12275 / 2.90 ( 4070) metal coordination : bond 0.00395 / 0.22 ( 23) metal coordination : angle 3.18571 / 1.50 ( 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 163 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6586 (mp) cc_final: 0.6252 (mm) REVERT: A 1014 LEU cc_start: 0.7629 (mt) cc_final: 0.7315 (tp) REVERT: A 1071 ARG cc_start: 0.3386 (mpp-170) cc_final: 0.2747 (tpt170) REVERT: A 1294 MET cc_start: 0.0886 (mtm) cc_final: 0.0535 (ptp) REVERT: A 1345 HIS cc_start: -0.0318 (t-90) cc_final: -0.1154 (m170) REVERT: B 247 TYR cc_start: 0.8188 (t80) cc_final: 0.7792 (t80) REVERT: C 347 MET cc_start: -0.3951 (tpt) cc_final: -0.4446 (tmm) REVERT: C 362 PHE cc_start: 0.5948 (t80) cc_final: 0.5633 (t80) REVERT: F 560 MET cc_start: 0.2518 (tpt) cc_final: 0.2242 (ttp) REVERT: b 59 LYS cc_start: 0.8737 (ptmt) cc_final: 0.8358 (pttm) REVERT: b 85 ASP cc_start: 0.8564 (m-30) cc_final: 0.8276 (p0) REVERT: c 38 ASN cc_start: 0.8697 (m-40) cc_final: 0.8285 (m110) REVERT: c 62 ILE cc_start: 0.8977 (tt) cc_final: 0.8744 (mm) REVERT: d 62 MET cc_start: 0.8733 (mmm) cc_final: 0.8495 (mmm) REVERT: e 60 LEU cc_start: 0.7743 (mt) cc_final: 0.7161 (pp) REVERT: g 56 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8195 (mm-30) REVERT: h 101 LEU cc_start: 0.8902 (mt) cc_final: 0.8673 (tp) REVERT: G 22 MET cc_start: 0.2226 (mmm) cc_final: 0.2026 (mtp) REVERT: G 113 ASN cc_start: 0.3461 (m-40) cc_final: 0.3109 (p0) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.1724 time to fit residues: 46.6206 Evaluate side-chains 134 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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: 0.0570 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 136 optimal weight: 0.0970 chunk 115 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 overall best weight: 3.4302 ------------------------------------------------------------------------------- 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** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 GLN ** 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.090183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.062031 restraints weight = 249044.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.063615 restraints weight = 145321.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.064582 restraints weight = 103832.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.064806 restraints weight = 84069.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.065617 restraints weight = 76022.845| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.6416 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= 0.454 Angle : 0.670 23.666 40465 Z= 0.374 Chirality : 0.043 0.198 4466 Planarity : 0.004 0.061 4129 Dihedral : 26.703 89.588 6239 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % 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: 0.08 (0.16), residues: 2646 helix: 1.11 (0.13), residues: 1552 sheet: -0.64 (0.48), residues: 114 loop : -1.60 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 564 TYR 0.025 0.001 TYR F 372 PHE 0.061 0.002 PHE E 387 TRP 0.043 0.002 TRP D 236 HIS 0.013 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.01035 / 0.45 (29033) covalent geometry : angle 0.66680 / 0.37 (40447) hydrogen bonds : bond 0.04880 / 3.22 ( 1499) hydrogen bonds : angle 4.02972 / 2.85 ( 4070) metal coordination : bond 0.00388 / 0.22 ( 23) metal coordination : angle 2.93286 / 1.40 ( 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 168 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.4651 (mtm) cc_final: 0.4430 (ptp) REVERT: A 1014 LEU cc_start: 0.7633 (mt) cc_final: 0.7339 (tp) REVERT: A 1294 MET cc_start: 0.0770 (mtm) cc_final: 0.0447 (ptp) REVERT: A 1345 HIS cc_start: -0.0221 (t-90) cc_final: -0.1026 (m170) REVERT: E 560 MET cc_start: 0.1949 (mmm) cc_final: 0.1444 (mmp) REVERT: B 247 TYR cc_start: 0.8261 (t80) cc_final: 0.7848 (t80) REVERT: C 347 MET cc_start: -0.3967 (tpt) cc_final: -0.4499 (tmm) REVERT: F 560 MET cc_start: 0.2561 (tpt) cc_final: 0.2221 (ttp) REVERT: b 59 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8350 (pttm) REVERT: b 85 ASP cc_start: 0.8731 (m-30) cc_final: 0.8211 (p0) REVERT: c 13 LYS cc_start: 0.6242 (tptm) cc_final: 0.5360 (mmmt) REVERT: c 38 ASN cc_start: 0.8697 (m-40) cc_final: 0.8399 (m110) REVERT: c 39 TYR cc_start: 0.8793 (m-80) cc_final: 0.8209 (m-80) REVERT: e 60 LEU cc_start: 0.7751 (mt) cc_final: 0.7174 (pp) REVERT: g 56 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8174 (mm-30) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1555 time to fit residues: 43.7320 Evaluate side-chains 134 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 162 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** E 302 HIS ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.089232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.061738 restraints weight = 250777.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.063347 restraints weight = 145438.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.064364 restraints weight = 102745.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.064616 restraints weight = 82286.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.065416 restraints weight = 72420.109| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6570 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= 0.451 Angle : 0.655 23.707 40465 Z= 0.367 Chirality : 0.043 0.230 4466 Planarity : 0.004 0.056 4129 Dihedral : 26.643 89.520 6239 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 0.04 % Allowed : 0.13 % Favored : 99.83 % 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: 0.19 (0.16), residues: 2646 helix: 1.20 (0.13), residues: 1552 sheet: -0.60 (0.49), residues: 113 loop : -1.57 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 564 TYR 0.025 0.001 TYR F 372 PHE 0.060 0.002 PHE E 387 TRP 0.042 0.002 TRP D 236 HIS 0.008 0.001 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01029 / 0.45 (29033) covalent geometry : angle 0.65148 / 0.37 (40447) hydrogen bonds : bond 0.04643 / 3.07 ( 1499) hydrogen bonds : angle 3.97131 / 2.80 ( 4070) metal coordination : bond 0.00769 / 0.43 ( 23) metal coordination : angle 3.06021 / 1.46 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9201.97 seconds wall clock time: 157 minutes 31.15 seconds (9451.15 seconds total)