Starting phenix.real_space_refine on Sun Jul 5 11:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9d_37365/07_2026/8w9d_37365_neut.cif" } resolution = 3.9 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16874 2.51 5 N 4918 2.21 5 O 5793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 265 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: 27990 Number of models: 1 Model: "" Number of chains: 21 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: 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: "c" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 857 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 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: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 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 95.945 97.988 84.400 1.00 41.65 S ATOM 5555 SG CYS E 266 93.206 96.692 86.613 1.00 37.12 S ATOM 5708 SG CYS E 286 96.717 95.119 87.251 1.00 32.48 S ATOM 5619 SG CYS E 275 104.117 103.028 76.035 1.00 75.04 S ATOM 5640 SG CYS E 278 101.718 102.280 74.106 1.00 80.64 S ATOM 5843 SG CYS E 303 103.082 99.150 74.710 1.00 77.29 S ATOM 5866 SG CYS E 306 103.956 101.507 71.469 1.00 87.59 S ATOM 6956 SG CYS E 440 62.238 85.587 102.105 1.00 43.56 S ATOM 6982 SG CYS E 443 59.142 83.263 101.859 1.00 42.11 S ATOM 6768 SG CYS E 417 55.505 87.436 112.700 1.00 31.16 S ATOM 6795 SG CYS E 420 53.328 87.794 115.635 1.00 34.53 S ATOM 7051 SG CYS E 451 57.329 87.185 116.091 1.00 35.06 S ATOM 14146 SG CYS F 275 50.062 45.721 55.986 1.00189.31 S ATOM 14370 SG CYS F 303 51.124 42.019 59.711 1.00186.67 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU b 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU b 22 " occ=0.00 residue: pdb=" N ARG b 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG b 23 " occ=0.00 Time building chain proxies: 5.34, per 1000 atoms: 0.19 Number of scatterers: 27990 At special positions: 0 Unit cell: (142.397, 200.008, 159.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 K 2 19.00 S 104 16.00 P 292 15.00 O 5793 8.00 N 4918 7.00 C 16874 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: 2.16 Conformation dependent library (CDL) restraints added in 778.9 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 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " 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 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 469 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 417 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 12 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 22 sheets defined 58.4% alpha, 5.0% beta 147 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.721A pdb=" N GLY A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.728A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.529A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.899A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 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 924 removed outlier: 4.003A pdb=" N THR A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 4.569A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.042A pdb=" N ASP A 929 " --> pdb=" O LYS A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 4.194A pdb=" N LYS A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 4.005A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.577A pdb=" N PHE A1022 " --> pdb=" O ILE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.626A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 4.102A pdb=" N TYR A1074 " --> pdb=" O HIS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.766A pdb=" N GLN A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 4.778A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.913A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.840A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.867A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.890A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1341 Processing helix chain 'E' and resid 303 through 312 Processing helix chain 'E' and resid 315 through 330 removed outlier: 3.515A pdb=" N LEU E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' 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 Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.792A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 579 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.667A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 60 " --> pdb=" O LEU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.324A pdb=" N GLU B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.597A pdb=" N ASN B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.846A 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 removed outlier: 3.775A pdb=" N LYS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 288 through 301 removed outlier: 4.745A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.660A pdb=" N VAL B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.546A pdb=" N TYR B 347 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.758A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.892A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.890A 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 349 through 374 removed outlier: 5.264A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.563A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 271 through 292 removed outlier: 3.635A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.686A 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 374 removed outlier: 4.400A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.587A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (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 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.930A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 3.848A pdb=" N THR F 360 " --> pdb=" O ILE F 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 361 " --> pdb=" O LYS F 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 361' Processing helix chain 'F' and resid 544 through 576 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.568A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.529A pdb=" N VAL a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.523A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.967A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 92 removed outlier: 3.582A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.542A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 72 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.618A 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 'd' and resid 37 through 49 Processing helix chain 'd' and resid 56 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 124 removed outlier: 3.728A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.579A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.559A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.597A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.967A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 92 removed outlier: 3.581A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.487A 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 91 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 4.034A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 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: 4.215A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 179 removed outlier: 3.695A pdb=" N GLU E 177 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG B 65 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 179 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 62 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.828A 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 505 through 506 removed outlier: 6.649A pdb=" N TYR E 506 " --> pdb=" O GLN E 541 " (cutoff:3.500A) 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: 7.231A 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 removed outlier: 3.614A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.511A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.215A 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: 3.566A 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 100 through 102 removed outlier: 6.585A 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: 6.741A 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: 7.423A 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: 3.605A 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: 6.852A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.792A 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) 1128 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 9.91 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 61 1.17 - 1.33: 5887 1.33 - 1.49: 11926 1.49 - 1.66: 11118 1.66 - 1.82: 159 Bond restraints: 29151 Sorted by residual: bond pdb=" C GLU A 920 " pdb=" O GLU A 920 " ideal model delta sigma weight residual 1.237 1.006 0.231 1.19e-02 7.06e+03 3.76e+02 bond pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 1.466 1.691 -0.225 1.21e-02 6.83e+03 3.46e+02 bond pdb=" C PRO B 42 " pdb=" O PRO B 42 " ideal model delta sigma weight residual 1.236 1.012 0.225 1.36e-02 5.41e+03 2.73e+02 bond pdb=" C PRO B 68 " pdb=" O PRO B 68 " ideal model delta sigma weight residual 1.234 1.048 0.186 1.14e-02 7.69e+03 2.66e+02 bond pdb=" C SER B 158 " pdb=" O SER B 158 " ideal model delta sigma weight residual 1.234 1.038 0.196 1.22e-02 6.72e+03 2.57e+02 ... (remaining 29146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.47: 40408 6.47 - 12.95: 167 12.95 - 19.42: 21 19.42 - 25.89: 1 25.89 - 32.36: 1 Bond angle restraints: 40598 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 109.65 142.01 -32.36 1.74e+00 3.30e-01 3.46e+02 angle pdb=" O ILE E 379 " pdb=" C ILE E 379 " pdb=" N PRO E 380 " ideal model delta sigma weight residual 121.10 102.94 18.16 1.14e+00 7.69e-01 2.54e+02 angle pdb=" C ARG B 136 " pdb=" N GLY B 137 " pdb=" CA GLY B 137 " ideal model delta sigma weight residual 121.51 139.52 -18.01 1.52e+00 4.33e-01 1.40e+02 angle pdb=" CA ILE E 379 " pdb=" C ILE E 379 " pdb=" N PRO E 380 " ideal model delta sigma weight residual 118.88 135.17 -16.29 1.54e+00 4.22e-01 1.12e+02 angle pdb=" C GLU B 129 " pdb=" CA GLU B 129 " pdb=" CB GLU B 129 " ideal model delta sigma weight residual 110.85 92.93 17.92 1.70e+00 3.46e-01 1.11e+02 ... (remaining 40593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 12687 18.74 - 37.48: 2295 37.48 - 56.22: 1609 56.22 - 74.96: 293 74.96 - 93.70: 35 Dihedral angle restraints: 16919 sinusoidal: 8968 harmonic: 7951 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 -152.24 30.24 0 2.50e+00 1.60e-01 1.46e+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 123.40 151.01 -27.61 0 2.50e+00 1.60e-01 1.22e+02 ... (remaining 16916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4431 0.239 - 0.477: 38 0.477 - 0.716: 9 0.716 - 0.954: 3 0.954 - 1.193: 3 Chirality restraints: 4484 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 1.19 2.00e-01 2.50e+01 3.56e+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 TYR B 313 " pdb=" N TYR B 313 " pdb=" C TYR B 313 " pdb=" CB TYR B 313 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 4481 not shown) Planarity restraints: 4146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 135 " 0.042 2.00e-02 2.50e+03 8.02e-02 6.44e+01 pdb=" C ASN B 135 " -0.139 2.00e-02 2.50e+03 pdb=" O ASN B 135 " 0.050 2.00e-02 2.50e+03 pdb=" N ARG B 136 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 70 " 0.033 2.00e-02 2.50e+03 6.80e-02 4.63e+01 pdb=" C THR B 70 " -0.118 2.00e-02 2.50e+03 pdb=" O THR B 70 " 0.046 2.00e-02 2.50e+03 pdb=" N LYS B 71 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 132 " 0.030 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C ALA B 132 " -0.109 2.00e-02 2.50e+03 pdb=" O ALA B 132 " 0.042 2.00e-02 2.50e+03 pdb=" N ARG B 133 " 0.037 2.00e-02 2.50e+03 ... (remaining 4143 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 19 2.22 - 2.95: 12204 2.95 - 3.68: 48048 3.68 - 4.41: 84775 4.41 - 5.14: 133386 Nonbonded interactions: 278432 Sorted by model distance: nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.489 3.860 nonbonded pdb=" NH1 ARG d 31 " pdb=" OP1 DA j 51 " model vdw 1.593 3.120 nonbonded pdb=" OE2 GLU E 178 " pdb=" NH1 ARG B 65 " model vdw 1.674 3.120 nonbonded pdb=" OG1 THR E 184 " pdb=" OE2 GLU B 73 " model vdw 1.685 3.040 nonbonded pdb=" OD1 ASP B 184 " pdb=" K K B1001 " model vdw 1.873 3.590 ... (remaining 278427 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' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 13 through 118) } 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=0.00 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.870 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 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 0.659 29170 Z= 0.804 Angle : 1.206 37.221 40610 Z= 0.833 Chirality : 0.075 1.193 4484 Planarity : 0.007 0.118 4146 Dihedral : 24.445 93.697 11779 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.90 % Favored : 94.42 % Rotamer: Outliers : 8.35 % Allowed : 22.48 % Favored : 69.17 % Cbeta Deviations : 1.87 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 2654 helix: -0.77 (0.12), residues: 1482 sheet: -1.35 (0.47), residues: 113 loop : -2.61 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 917 TYR 0.063 0.002 TYR B 176 PHE 0.048 0.002 PHE E 387 TRP 0.059 0.005 TRP E 301 HIS 0.009 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.01067 / 0.77 (29151) covalent geometry : angle 1.17875 / 0.83 (40598) hydrogen bonds : bond 0.13165 / 8.63 ( 1482) hydrogen bonds : angle 5.23737 / 3.74 ( 4035) metal coordination : bond 0.28420 / 17.33 ( 19) metal coordination : angle 14.82780 / 8.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 605 time to evaluate : 0.785 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: A 691 LEU cc_start: 0.7374 (mt) cc_final: 0.6939 (tt) REVERT: A 702 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7298 (tp) REVERT: A 837 LYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4740 (mptp) REVERT: A 867 ILE cc_start: 0.7426 (mt) cc_final: 0.6604 (mm) REVERT: A 934 THR cc_start: 0.6454 (OUTLIER) cc_final: 0.5872 (t) REVERT: A 1069 LEU cc_start: -0.1619 (OUTLIER) cc_final: -0.2655 (mt) REVERT: A 1261 LYS cc_start: 0.5672 (mmtt) cc_final: 0.5441 (mmtp) REVERT: A 1286 TYR cc_start: 0.5571 (t80) cc_final: 0.5349 (t80) REVERT: E 105 ASP cc_start: -0.4256 (OUTLIER) cc_final: -0.4799 (t70) REVERT: E 318 THR cc_start: 0.4647 (p) cc_final: 0.4284 (m) REVERT: E 386 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4573 (tp) REVERT: E 468 LEU cc_start: 0.5290 (mt) cc_final: 0.5089 (mt) REVERT: E 491 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6422 (p) REVERT: E 569 PHE cc_start: 0.3812 (t80) cc_final: 0.3252 (t80) REVERT: B 40 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3898 (tpt) REVERT: B 74 MET cc_start: 0.5258 (mtt) cc_final: 0.5055 (mtt) REVERT: C 364 VAL cc_start: 0.7964 (m) cc_final: 0.7623 (p) REVERT: D 217 THR cc_start: 0.2408 (OUTLIER) cc_final: 0.1764 (t) REVERT: D 325 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3283 (mp) REVERT: D 337 VAL cc_start: 0.6224 (OUTLIER) cc_final: 0.5562 (t) REVERT: D 345 THR cc_start: 0.6046 (OUTLIER) cc_final: 0.5753 (t) REVERT: D 353 GLN cc_start: 0.8450 (tt0) cc_final: 0.8026 (mt0) REVERT: F 546 SER cc_start: 0.7318 (t) cc_final: 0.7033 (p) REVERT: F 556 TYR cc_start: 0.4570 (t80) cc_final: 0.3802 (t80) REVERT: a 120 MET cc_start: 0.7471 (mtt) cc_final: 0.6944 (mtt) REVERT: b 88 TYR cc_start: 0.7865 (m-10) cc_final: 0.6765 (m-80) REVERT: d 87 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6798 (t) REVERT: G 22 MET cc_start: 0.0044 (mtm) cc_final: -0.1044 (tpp) outliers start: 201 outliers final: 26 residues processed: 751 average time/residue: 0.2039 time to fit residues: 234.1283 Evaluate side-chains 290 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 PRO Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 492 TRP Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 346 HIS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 87 SER Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 11 ARG Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 ASN A 690 ASN A 722 ASN ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A 961 ASN A1038 GLN A1216 ASN ** A1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 346 HIS E 376 ASN E 433 ASN E 495 GLN E 503 GLN E 510 GLN ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN B 291 HIS B 364 ASN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN D 277 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN D 358 GLN D 369 HIS F 259 ASN F 283 HIS F 294 ASN F 329 GLN F 332 ASN F 350 GLN F 568 GLN a 39 HIS b 75 HIS b 93 GLN c 38 ASN c 73 ASN c 112 GLN e 5 GLN e 39 HIS e 76 GLN e 125 GLN g 31 HIS g 73 ASN h 47 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.114718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.093837 restraints weight = 125427.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.093321 restraints weight = 109648.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093909 restraints weight = 80657.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.093897 restraints weight = 66782.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.093917 restraints weight = 68433.766| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 2.098 29170 Z= 0.449 Angle : 0.823 32.812 40610 Z= 0.433 Chirality : 0.049 0.506 4484 Planarity : 0.006 0.112 4146 Dihedral : 26.474 84.376 6325 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.48 % Rotamer: Outliers : 5.36 % Allowed : 24.01 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -1.08 (0.16), residues: 2654 helix: 0.31 (0.13), residues: 1507 sheet: -0.96 (0.50), residues: 102 loop : -2.24 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 182 TYR 0.030 0.002 TYR A1016 PHE 0.028 0.002 PHE B 377 TRP 0.027 0.002 TRP C 236 HIS 0.011 0.001 HIS A1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (29151) covalent geometry : angle 0.79556 / 0.43 (40598) hydrogen bonds : bond 0.06158 / 4.00 ( 1482) hydrogen bonds : angle 4.31845 / 3.07 ( 4035) metal coordination : bond 0.48159 / 37.04 ( 19) metal coordination : angle 12.34009 / 7.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 277 time to evaluate : 0.977 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: A 691 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6958 (tp) REVERT: A 901 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6695 (mmmt) REVERT: A 962 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4407 (tptt) REVERT: A 1004 ASN cc_start: 0.6577 (m-40) cc_final: 0.6064 (t0) REVERT: A 1069 LEU cc_start: -0.2122 (OUTLIER) cc_final: -0.2726 (mt) REVERT: A 1294 MET cc_start: 0.3939 (ptt) cc_final: 0.3738 (ptp) REVERT: A 1325 LYS cc_start: -0.3581 (OUTLIER) cc_final: -0.3833 (tppt) REVERT: E 125 ARG cc_start: 0.4492 (mtp180) cc_final: 0.4122 (ptp90) REVERT: E 345 SER cc_start: 0.3392 (OUTLIER) cc_final: 0.2682 (m) REVERT: E 384 ARG cc_start: 0.3447 (OUTLIER) cc_final: 0.3210 (mpt180) REVERT: E 385 GLN cc_start: 0.4093 (tp-100) cc_final: 0.3801 (tp-100) REVERT: E 512 ILE cc_start: 0.4414 (OUTLIER) cc_final: 0.4156 (mm) REVERT: E 569 PHE cc_start: 0.3893 (t80) cc_final: 0.3381 (t80) REVERT: B 53 MET cc_start: 0.7031 (mmm) cc_final: 0.6756 (mmm) REVERT: C 364 VAL cc_start: 0.9058 (m) cc_final: 0.8836 (p) REVERT: D 353 GLN cc_start: 0.8378 (tt0) cc_final: 0.7951 (mt0) REVERT: b 44 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8235 (tttm) REVERT: b 50 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7798 (mm) REVERT: G 22 MET cc_start: -0.0474 (mtm) cc_final: -0.0905 (tpp) outliers start: 129 outliers final: 46 residues processed: 372 average time/residue: 0.1740 time to fit residues: 104.4167 Evaluate side-chains 266 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 492 TRP Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain a residue 123 ASP Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 226 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 274 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1127 GLN A1165 ASN A1289 GLN E 342 ASN E 346 HIS E 499 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN F 346 HIS a 76 GLN c 73 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.114041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.092320 restraints weight = 124553.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.091972 restraints weight = 100238.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.092760 restraints weight = 75109.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.092539 restraints weight = 62953.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092626 restraints weight = 64874.713| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29170 Z= 0.164 Angle : 0.724 11.380 40610 Z= 0.392 Chirality : 0.045 0.383 4484 Planarity : 0.005 0.135 4146 Dihedral : 26.244 81.964 6275 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 4.45 % Allowed : 23.76 % Favored : 71.79 % 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: -0.47 (0.16), residues: 2654 helix: 0.82 (0.13), residues: 1492 sheet: -0.94 (0.54), residues: 88 loop : -1.93 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 182 TYR 0.026 0.002 TYR d 83 PHE 0.028 0.002 PHE B 377 TRP 0.047 0.002 TRP C 236 HIS 0.030 0.001 HIS F 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (29151) covalent geometry : angle 0.71779 / 0.39 (40598) hydrogen bonds : bond 0.05458 / 3.50 ( 1482) hydrogen bonds : angle 4.09917 / 2.90 ( 4035) metal coordination : bond 0.02032 / 1.51 ( 19) metal coordination : angle 5.61506 / 3.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 251 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LEU cc_start: 0.7456 (mt) cc_final: 0.6920 (tt) REVERT: A 1004 ASN cc_start: 0.6713 (m-40) cc_final: 0.6125 (t0) REVERT: A 1068 ILE cc_start: 0.3180 (mt) cc_final: 0.2821 (tp) REVERT: A 1069 LEU cc_start: -0.2252 (OUTLIER) cc_final: -0.2606 (mt) REVERT: A 1325 LYS cc_start: -0.3387 (OUTLIER) cc_final: -0.3707 (tppt) REVERT: E 125 ARG cc_start: 0.4638 (mtp180) cc_final: 0.3882 (tpp-160) REVERT: E 358 LYS cc_start: 0.6454 (mtmt) cc_final: 0.6157 (ttmt) REVERT: E 371 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: E 390 SER cc_start: 0.4577 (OUTLIER) cc_final: 0.4270 (t) REVERT: E 512 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.4339 (mm) REVERT: E 569 PHE cc_start: 0.3629 (t80) cc_final: 0.3067 (t80) REVERT: B 61 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5147 (tmm) REVERT: B 87 SER cc_start: 0.3158 (OUTLIER) cc_final: 0.2926 (p) REVERT: B 96 MET cc_start: 0.7658 (ttm) cc_final: 0.7423 (ttm) REVERT: B 334 LEU cc_start: 0.7072 (mm) cc_final: 0.6776 (mm) REVERT: D 303 ARG cc_start: 0.4010 (mtm180) cc_final: 0.3766 (ttm170) REVERT: D 353 GLN cc_start: 0.8480 (tt0) cc_final: 0.8029 (mt0) REVERT: F 287 LEU cc_start: 0.4192 (mp) cc_final: 0.3493 (tp) REVERT: F 316 MET cc_start: 0.4947 (mmm) cc_final: 0.4627 (mmm) REVERT: b 44 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8302 (tttm) REVERT: b 50 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7888 (mm) REVERT: c 17 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7833 (mtm-85) REVERT: d 62 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: G 22 MET cc_start: -0.0358 (mtm) cc_final: -0.0606 (tpp) outliers start: 107 outliers final: 58 residues processed: 326 average time/residue: 0.1689 time to fit residues: 89.5233 Evaluate side-chains 279 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 15 LYS Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 73 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 41 VAL Chi-restraints excluded: chain h residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 45 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 266 optimal weight: 40.0000 chunk 95 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 HIS E 346 HIS E 499 ASN E 519 ASN E 521 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 GLN F 268 GLN c 104 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 82 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.110322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.088586 restraints weight = 123008.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.088589 restraints weight = 96846.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.088750 restraints weight = 76634.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.088788 restraints weight = 68741.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.088828 restraints weight = 61495.842| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29170 Z= 0.246 Angle : 0.807 11.518 40610 Z= 0.436 Chirality : 0.048 0.308 4484 Planarity : 0.006 0.140 4146 Dihedral : 26.409 84.293 6267 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 5.86 % Allowed : 22.64 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.62 (0.16), residues: 2654 helix: 0.56 (0.13), residues: 1524 sheet: -1.27 (0.53), residues: 88 loop : -1.80 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 88 TYR 0.043 0.003 TYR d 83 PHE 0.036 0.003 PHE B 377 TRP 0.024 0.002 TRP E 492 HIS 0.010 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 (29151) covalent geometry : angle 0.80026 / 0.44 (40598) hydrogen bonds : bond 0.06907 / 4.43 ( 1482) hydrogen bonds : angle 4.28874 / 3.04 ( 4035) metal coordination : bond 0.01803 / 1.24 ( 19) metal coordination : angle 6.02026 / 3.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 229 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 901 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6630 (mmmt) REVERT: A 956 LYS cc_start: 0.7879 (tttm) cc_final: 0.7446 (ptmm) REVERT: A 971 PRO cc_start: -0.0514 (Cg_endo) cc_final: -0.0742 (Cg_exo) REVERT: A 1004 ASN cc_start: 0.6825 (m-40) cc_final: 0.6162 (t0) REVERT: A 1068 ILE cc_start: 0.3560 (mt) cc_final: 0.3281 (tp) REVERT: A 1069 LEU cc_start: -0.2595 (OUTLIER) cc_final: -0.3123 (mt) REVERT: A 1294 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.4284 (ptp) REVERT: A 1325 LYS cc_start: -0.3497 (OUTLIER) cc_final: -0.3968 (tppt) REVERT: E 280 LYS cc_start: 0.3353 (OUTLIER) cc_final: 0.2620 (pttm) REVERT: E 339 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5622 (mt) REVERT: E 358 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5977 (ttmt) REVERT: E 371 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: E 390 SER cc_start: 0.4609 (OUTLIER) cc_final: 0.4262 (t) REVERT: E 560 MET cc_start: 0.5694 (mmp) cc_final: 0.5187 (tpp) REVERT: B 96 MET cc_start: 0.7575 (ttm) cc_final: 0.7344 (ttm) REVERT: C 242 ASP cc_start: 0.6804 (m-30) cc_final: 0.6493 (m-30) REVERT: D 324 ARG cc_start: 0.5639 (mmm160) cc_final: 0.4692 (ptt180) REVERT: D 353 GLN cc_start: 0.8554 (tt0) cc_final: 0.8012 (mt0) REVERT: D 355 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6461 (mt) REVERT: F 266 CYS cc_start: 0.1435 (OUTLIER) cc_final: 0.0879 (p) REVERT: F 287 LEU cc_start: 0.4496 (mp) cc_final: 0.3696 (tp) REVERT: c 64 GLU cc_start: 0.7954 (pp20) cc_final: 0.6858 (pt0) REVERT: d 62 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: e 81 ASP cc_start: 0.7054 (t0) cc_final: 0.6796 (p0) REVERT: G 22 MET cc_start: -0.0753 (mtm) cc_final: -0.0991 (tmm) outliers start: 141 outliers final: 75 residues processed: 340 average time/residue: 0.1742 time to fit residues: 97.5995 Evaluate side-chains 278 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain a residue 123 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 118 THR Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 41 VAL Chi-restraints excluded: chain h residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 151 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 241 optimal weight: 0.4980 chunk 55 optimal weight: 30.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1075 GLN A1165 ASN A1216 ASN E 346 HIS E 499 ASN E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN C 358 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN F 371 GLN c 73 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.091043 restraints weight = 124086.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090870 restraints weight = 117083.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.091181 restraints weight = 91050.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091270 restraints weight = 78515.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091247 restraints weight = 75641.685| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29170 Z= 0.180 Angle : 0.716 10.164 40610 Z= 0.388 Chirality : 0.046 0.304 4484 Planarity : 0.005 0.125 4146 Dihedral : 26.319 82.327 6262 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 4.57 % Allowed : 24.10 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -0.31 (0.16), residues: 2654 helix: 0.85 (0.13), residues: 1520 sheet: -1.30 (0.52), residues: 88 loop : -1.70 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 770 TYR 0.028 0.002 TYR d 83 PHE 0.070 0.002 PHE B 377 TRP 0.021 0.002 TRP C 236 HIS 0.010 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (29151) covalent geometry : angle 0.71055 / 0.39 (40598) hydrogen bonds : bond 0.05429 / 3.52 ( 1482) hydrogen bonds : angle 4.07064 / 2.88 ( 4035) metal coordination : bond 0.01257 / 0.84 ( 19) metal coordination : angle 5.00510 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 212 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 901 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6582 (mmmt) REVERT: A 956 LYS cc_start: 0.7699 (tttm) cc_final: 0.7230 (ptmm) REVERT: A 971 PRO cc_start: -0.0294 (Cg_endo) cc_final: -0.0510 (Cg_exo) REVERT: A 1004 ASN cc_start: 0.6840 (m-40) cc_final: 0.6069 (t0) REVERT: A 1068 ILE cc_start: 0.3555 (mt) cc_final: 0.3165 (tp) REVERT: A 1069 LEU cc_start: -0.2696 (OUTLIER) cc_final: -0.3058 (mt) REVERT: E 125 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.3650 (tpt170) REVERT: E 316 MET cc_start: 0.4293 (pmm) cc_final: 0.3776 (pmm) REVERT: E 339 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5783 (mt) REVERT: E 390 SER cc_start: 0.5093 (OUTLIER) cc_final: 0.4728 (t) REVERT: E 560 MET cc_start: 0.5793 (mmp) cc_final: 0.5310 (tpp) REVERT: E 562 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.5336 (pt0) REVERT: B 286 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5959 (tp) REVERT: C 381 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6231 (ttm110) REVERT: D 303 ARG cc_start: 0.4407 (mtm180) cc_final: 0.4012 (ttm170) REVERT: D 324 ARG cc_start: 0.5488 (mmm160) cc_final: 0.4453 (ptt180) REVERT: D 353 GLN cc_start: 0.8419 (tt0) cc_final: 0.7887 (mt0) REVERT: D 355 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6682 (mt) REVERT: F 266 CYS cc_start: 0.1631 (OUTLIER) cc_final: 0.1165 (p) REVERT: F 287 LEU cc_start: 0.4277 (mp) cc_final: 0.3504 (tp) REVERT: b 44 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8310 (tttm) REVERT: c 64 GLU cc_start: 0.7939 (pp20) cc_final: 0.6946 (pt0) REVERT: e 5 GLN cc_start: 0.2940 (mt0) cc_final: 0.2495 (mt0) REVERT: g 41 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6398 (mm-30) REVERT: h 90 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7041 (p) outliers start: 110 outliers final: 62 residues processed: 300 average time/residue: 0.1703 time to fit residues: 84.2765 Evaluate side-chains 261 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 15 LYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 73 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 11 ARG Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 41 VAL Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 130 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 260 optimal weight: 40.0000 chunk 199 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 346 HIS E 402 ASN E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS c 31 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.112011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.092241 restraints weight = 124618.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.091745 restraints weight = 129356.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.092216 restraints weight = 104161.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.092196 restraints weight = 83963.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.092264 restraints weight = 80496.010| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29170 Z= 0.135 Angle : 0.668 9.656 40610 Z= 0.364 Chirality : 0.043 0.247 4484 Planarity : 0.004 0.118 4146 Dihedral : 26.138 80.925 6262 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 3.45 % Allowed : 25.22 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: 2654 helix: 1.09 (0.13), residues: 1522 sheet: -1.01 (0.53), residues: 88 loop : -1.53 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 770 TYR 0.048 0.001 TYR d 83 PHE 0.049 0.001 PHE B 377 TRP 0.022 0.001 TRP A 719 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (29151) covalent geometry : angle 0.66392 / 0.36 (40598) hydrogen bonds : bond 0.04784 / 3.11 ( 1482) hydrogen bonds : angle 3.89362 / 2.76 ( 4035) metal coordination : bond 0.00632 / 0.41 ( 19) metal coordination : angle 4.08075 / 2.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.8005 (tt) cc_final: 0.7804 (tt) REVERT: A 875 ARG cc_start: 0.5584 (mpp80) cc_final: 0.3920 (ptt90) REVERT: A 901 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6324 (mmmt) REVERT: A 971 PRO cc_start: -0.0839 (Cg_endo) cc_final: -0.1065 (Cg_exo) REVERT: A 1004 ASN cc_start: 0.6929 (m-40) cc_final: 0.6187 (t0) REVERT: A 1068 ILE cc_start: 0.3331 (OUTLIER) cc_final: 0.3013 (tp) REVERT: A 1069 LEU cc_start: -0.2691 (OUTLIER) cc_final: -0.3112 (mt) REVERT: A 1199 VAL cc_start: 0.3397 (OUTLIER) cc_final: 0.3090 (p) REVERT: E 280 LYS cc_start: 0.3190 (OUTLIER) cc_final: 0.2443 (pttm) REVERT: E 316 MET cc_start: 0.4345 (pmm) cc_final: 0.3885 (pmm) REVERT: E 339 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5876 (mt) REVERT: E 390 SER cc_start: 0.4831 (OUTLIER) cc_final: 0.4543 (t) REVERT: E 560 MET cc_start: 0.5781 (mmp) cc_final: 0.5282 (tpp) REVERT: D 303 ARG cc_start: 0.4366 (mtm180) cc_final: 0.4017 (ttm170) REVERT: D 324 ARG cc_start: 0.5620 (mmm160) cc_final: 0.5289 (mmp-170) REVERT: D 353 GLN cc_start: 0.8433 (tt0) cc_final: 0.7898 (mt0) REVERT: D 355 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6573 (mt) REVERT: F 266 CYS cc_start: 0.1572 (OUTLIER) cc_final: 0.1099 (p) REVERT: F 287 LEU cc_start: 0.4171 (mp) cc_final: 0.3554 (tp) REVERT: b 44 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8223 (tttm) REVERT: c 64 GLU cc_start: 0.7843 (pp20) cc_final: 0.6999 (pt0) REVERT: d 62 MET cc_start: 0.7337 (mpp) cc_final: 0.7069 (mmp) REVERT: d 89 ILE cc_start: 0.6666 (mm) cc_final: 0.6408 (tp) REVERT: g 41 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6344 (mm-30) outliers start: 83 outliers final: 46 residues processed: 289 average time/residue: 0.1710 time to fit residues: 81.4782 Evaluate side-chains 257 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 163 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 167 optimal weight: 0.0050 chunk 35 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1289 GLN E 346 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.112536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.092917 restraints weight = 124690.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.093309 restraints weight = 109146.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093405 restraints weight = 87040.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.093215 restraints weight = 83729.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.093256 restraints weight = 77281.206| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29170 Z= 0.131 Angle : 0.649 11.732 40610 Z= 0.354 Chirality : 0.042 0.215 4484 Planarity : 0.004 0.140 4146 Dihedral : 25.950 81.355 6262 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 25.47 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: 0.33 (0.16), residues: 2654 helix: 1.32 (0.13), residues: 1520 sheet: -0.79 (0.50), residues: 102 loop : -1.37 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 770 TYR 0.038 0.001 TYR d 83 PHE 0.048 0.001 PHE B 377 TRP 0.024 0.001 TRP A 719 HIS 0.005 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (29151) covalent geometry : angle 0.64663 / 0.35 (40598) hydrogen bonds : bond 0.04391 / 2.84 ( 1482) hydrogen bonds : angle 3.77075 / 2.68 ( 4035) metal coordination : bond 0.00479 / 0.31 ( 19) metal coordination : angle 3.41505 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.8005 (tt) cc_final: 0.7762 (tt) REVERT: A 901 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6433 (mmmt) REVERT: A 1004 ASN cc_start: 0.6813 (m-40) cc_final: 0.6117 (t0) REVERT: A 1068 ILE cc_start: 0.3467 (OUTLIER) cc_final: 0.3138 (tp) REVERT: A 1069 LEU cc_start: -0.2852 (OUTLIER) cc_final: -0.3378 (mt) REVERT: A 1199 VAL cc_start: 0.3307 (OUTLIER) cc_final: 0.3080 (p) REVERT: E 280 LYS cc_start: 0.2903 (OUTLIER) cc_final: 0.2187 (pttm) REVERT: E 339 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5903 (mt) REVERT: E 503 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: E 516 ASN cc_start: 0.2350 (OUTLIER) cc_final: 0.1210 (t0) REVERT: E 560 MET cc_start: 0.5918 (mmp) cc_final: 0.5499 (tpp) REVERT: E 562 GLN cc_start: 0.5621 (OUTLIER) cc_final: 0.5379 (pt0) REVERT: B 61 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5670 (tmm) REVERT: B 96 MET cc_start: 0.7849 (ttm) cc_final: 0.7270 (mmm) REVERT: B 141 VAL cc_start: 0.7560 (t) cc_final: 0.7325 (t) REVERT: D 303 ARG cc_start: 0.4320 (mtm180) cc_final: 0.4057 (ttm170) REVERT: D 324 ARG cc_start: 0.5628 (mmm160) cc_final: 0.4774 (ptt180) REVERT: D 353 GLN cc_start: 0.8408 (tt0) cc_final: 0.7879 (mt0) REVERT: F 266 CYS cc_start: 0.1512 (OUTLIER) cc_final: 0.1057 (p) REVERT: F 274 CYS cc_start: -0.0625 (t) cc_final: -0.0976 (p) REVERT: F 287 LEU cc_start: 0.4091 (mp) cc_final: 0.3550 (tp) REVERT: b 44 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8226 (tttm) REVERT: c 64 GLU cc_start: 0.7781 (pp20) cc_final: 0.7010 (pt0) REVERT: d 62 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7051 (mmp) REVERT: e 80 THR cc_start: 0.7904 (m) cc_final: 0.7595 (m) REVERT: e 81 ASP cc_start: 0.6693 (t0) cc_final: 0.6393 (p0) REVERT: g 41 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6034 (mm-30) outliers start: 75 outliers final: 44 residues processed: 287 average time/residue: 0.1696 time to fit residues: 80.6289 Evaluate side-chains 263 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 260 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 256 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 HIS E 346 HIS E 519 ASN D 275 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.111266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.090727 restraints weight = 124256.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.090166 restraints weight = 124637.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.090650 restraints weight = 98922.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.090460 restraints weight = 89965.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090561 restraints weight = 84007.488| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29170 Z= 0.149 Angle : 0.669 14.619 40610 Z= 0.361 Chirality : 0.042 0.212 4484 Planarity : 0.005 0.146 4146 Dihedral : 25.971 83.026 6262 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.07 % Allowed : 25.59 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: 0.32 (0.16), residues: 2654 helix: 1.30 (0.13), residues: 1513 sheet: -0.79 (0.49), residues: 101 loop : -1.34 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 770 TYR 0.059 0.002 TYR d 83 PHE 0.040 0.002 PHE B 377 TRP 0.024 0.002 TRP E 301 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (29151) covalent geometry : angle 0.66604 / 0.36 (40598) hydrogen bonds : bond 0.04862 / 3.14 ( 1482) hydrogen bonds : angle 3.82185 / 2.72 ( 4035) metal coordination : bond 0.00812 / 0.54 ( 19) metal coordination : angle 3.93035 / 2.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 217 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 901 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6448 (mmmt) REVERT: A 956 LYS cc_start: 0.7741 (tttm) cc_final: 0.7277 (ptmm) REVERT: A 1004 ASN cc_start: 0.6869 (m-40) cc_final: 0.6130 (t0) REVERT: A 1068 ILE cc_start: 0.3757 (mt) cc_final: 0.3499 (tp) REVERT: A 1069 LEU cc_start: -0.2834 (OUTLIER) cc_final: -0.3385 (mm) REVERT: E 280 LYS cc_start: 0.3119 (OUTLIER) cc_final: 0.2433 (pttm) REVERT: E 339 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5917 (mt) REVERT: E 407 ILE cc_start: 0.7738 (mt) cc_final: 0.7526 (mm) REVERT: E 503 GLN cc_start: 0.5961 (OUTLIER) cc_final: 0.5158 (tm-30) REVERT: E 516 ASN cc_start: 0.2020 (OUTLIER) cc_final: 0.0821 (t0) REVERT: E 560 MET cc_start: 0.6081 (mmp) cc_final: 0.5646 (tpp) REVERT: E 562 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.5361 (pt0) REVERT: B 61 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5844 (tmm) REVERT: B 96 MET cc_start: 0.7823 (ttm) cc_final: 0.7346 (mmm) REVERT: D 303 ARG cc_start: 0.4404 (mtm180) cc_final: 0.4102 (ttm170) REVERT: D 324 ARG cc_start: 0.5671 (mmm160) cc_final: 0.4875 (ptt180) REVERT: D 353 GLN cc_start: 0.8411 (tt0) cc_final: 0.8001 (mp10) REVERT: F 266 CYS cc_start: 0.1433 (OUTLIER) cc_final: 0.0971 (p) REVERT: F 274 CYS cc_start: -0.1056 (t) cc_final: -0.1350 (p) REVERT: F 287 LEU cc_start: 0.4223 (mp) cc_final: 0.3685 (tp) REVERT: c 64 GLU cc_start: 0.7753 (pp20) cc_final: 0.6927 (pt0) REVERT: d 62 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7103 (mmp) REVERT: g 41 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6100 (mm-30) REVERT: h 80 LEU cc_start: 0.8325 (tt) cc_final: 0.8125 (tp) outliers start: 74 outliers final: 50 residues processed: 270 average time/residue: 0.1637 time to fit residues: 72.7918 Evaluate side-chains 268 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 264 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 519 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.111097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.091343 restraints weight = 124129.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.091349 restraints weight = 115504.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.091480 restraints weight = 93604.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.091511 restraints weight = 82533.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.091517 restraints weight = 75368.778| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29170 Z= 0.148 Angle : 0.673 14.965 40610 Z= 0.361 Chirality : 0.042 0.219 4484 Planarity : 0.005 0.147 4146 Dihedral : 25.977 82.780 6262 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 3.20 % Allowed : 25.51 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: 0.35 (0.16), residues: 2654 helix: 1.32 (0.13), residues: 1512 sheet: -0.70 (0.50), residues: 101 loop : -1.30 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 897 TYR 0.056 0.002 TYR d 83 PHE 0.041 0.002 PHE B 377 TRP 0.019 0.002 TRP A 719 HIS 0.005 0.001 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (29151) covalent geometry : angle 0.66835 / 0.36 (40598) hydrogen bonds : bond 0.04708 / 3.06 ( 1482) hydrogen bonds : angle 3.81504 / 2.71 ( 4035) metal coordination : bond 0.00828 / 0.55 ( 19) metal coordination : angle 4.60617 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 220 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 901 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6445 (mmmt) REVERT: A 956 LYS cc_start: 0.7718 (tttm) cc_final: 0.7250 (ptmm) REVERT: A 1004 ASN cc_start: 0.6982 (m-40) cc_final: 0.6283 (t0) REVERT: A 1068 ILE cc_start: 0.3628 (mt) cc_final: 0.2987 (tp) REVERT: E 280 LYS cc_start: 0.2951 (OUTLIER) cc_final: 0.2245 (pttm) REVERT: E 339 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5992 (mt) REVERT: E 407 ILE cc_start: 0.7682 (mt) cc_final: 0.7463 (mm) REVERT: E 503 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5127 (tm-30) REVERT: E 516 ASN cc_start: 0.1884 (OUTLIER) cc_final: 0.1268 (t0) REVERT: E 560 MET cc_start: 0.5955 (mmp) cc_final: 0.5568 (tpp) REVERT: B 96 MET cc_start: 0.7692 (ttm) cc_final: 0.7186 (mmm) REVERT: B 259 MET cc_start: 0.7673 (tmm) cc_final: 0.7446 (tmm) REVERT: D 303 ARG cc_start: 0.4227 (mtm180) cc_final: 0.3904 (ttm170) REVERT: D 324 ARG cc_start: 0.5568 (mmm160) cc_final: 0.5190 (mmp-170) REVERT: D 353 GLN cc_start: 0.8384 (tt0) cc_final: 0.8002 (mp10) REVERT: D 363 LEU cc_start: 0.5447 (pp) cc_final: 0.5244 (pp) REVERT: F 266 CYS cc_start: 0.1192 (OUTLIER) cc_final: 0.0838 (p) REVERT: F 274 CYS cc_start: -0.0749 (t) cc_final: -0.1196 (p) REVERT: F 287 LEU cc_start: 0.4083 (mp) cc_final: 0.3570 (tp) REVERT: c 64 GLU cc_start: 0.7746 (pp20) cc_final: 0.6925 (pt0) REVERT: d 62 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7135 (mmp) REVERT: f 50 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8184 (mm) REVERT: g 41 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6121 (mm-30) outliers start: 77 outliers final: 59 residues processed: 277 average time/residue: 0.1622 time to fit residues: 73.3744 Evaluate side-chains 270 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain g residue 11 ARG Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 402 ASN E 519 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.111768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.091958 restraints weight = 123416.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.091907 restraints weight = 122126.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.092060 restraints weight = 96118.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091955 restraints weight = 88738.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.092025 restraints weight = 77991.083| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29170 Z= 0.133 Angle : 0.670 15.480 40610 Z= 0.358 Chirality : 0.042 0.222 4484 Planarity : 0.005 0.148 4146 Dihedral : 25.912 82.375 6262 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 2.74 % Allowed : 25.84 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2654 helix: 1.39 (0.13), residues: 1510 sheet: -0.95 (0.47), residues: 111 loop : -1.23 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 239 TYR 0.049 0.001 TYR F 549 PHE 0.041 0.001 PHE B 377 TRP 0.019 0.001 TRP A 719 HIS 0.009 0.001 HIS F 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (29151) covalent geometry : angle 0.66562 / 0.36 (40598) hydrogen bonds : bond 0.04476 / 2.91 ( 1482) hydrogen bonds : angle 3.77257 / 2.69 ( 4035) metal coordination : bond 0.00638 / 0.42 ( 19) metal coordination : angle 4.59414 / 2.53 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 901 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6456 (mmmt) REVERT: A 956 LYS cc_start: 0.7699 (tttm) cc_final: 0.7220 (ptmm) REVERT: A 1004 ASN cc_start: 0.6960 (m-40) cc_final: 0.6250 (t0) REVERT: A 1068 ILE cc_start: 0.3089 (OUTLIER) cc_final: 0.2843 (tp) REVERT: E 280 LYS cc_start: 0.2993 (OUTLIER) cc_final: 0.2265 (pttm) REVERT: E 339 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5967 (mt) REVERT: E 407 ILE cc_start: 0.7678 (mt) cc_final: 0.7451 (mm) REVERT: E 503 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5145 (tm-30) REVERT: E 516 ASN cc_start: 0.2508 (OUTLIER) cc_final: 0.2107 (t0) REVERT: E 560 MET cc_start: 0.5907 (mmp) cc_final: 0.5527 (tpp) REVERT: B 61 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5526 (tmm) REVERT: B 96 MET cc_start: 0.7663 (ttm) cc_final: 0.7123 (mmm) REVERT: B 259 MET cc_start: 0.7683 (tmm) cc_final: 0.7458 (tmm) REVERT: D 303 ARG cc_start: 0.4176 (mtm180) cc_final: 0.3840 (ttm170) REVERT: D 324 ARG cc_start: 0.5574 (mmm160) cc_final: 0.5245 (mmp-170) REVERT: D 353 GLN cc_start: 0.8390 (tt0) cc_final: 0.7971 (mp10) REVERT: D 363 LEU cc_start: 0.5393 (pp) cc_final: 0.5163 (pp) REVERT: F 266 CYS cc_start: 0.0930 (OUTLIER) cc_final: 0.0624 (p) REVERT: F 274 CYS cc_start: -0.0549 (t) cc_final: -0.0900 (p) REVERT: F 287 LEU cc_start: 0.3991 (mp) cc_final: 0.3432 (tp) REVERT: a 90 MET cc_start: 0.6922 (mmm) cc_final: 0.6607 (mmt) REVERT: c 64 GLU cc_start: 0.7706 (pp20) cc_final: 0.6880 (pt0) REVERT: d 62 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7090 (mmp) REVERT: f 50 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (mm) REVERT: g 41 GLU cc_start: 0.6364 (mm-30) cc_final: 0.6088 (mm-30) outliers start: 66 outliers final: 50 residues processed: 267 average time/residue: 0.1725 time to fit residues: 75.1861 Evaluate side-chains 266 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 50 GLU Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain g residue 11 ARG Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 242 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 231 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 519 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.111892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090278 restraints weight = 122701.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.089854 restraints weight = 108532.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.090124 restraints weight = 86354.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.090170 restraints weight = 75845.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.090200 restraints weight = 71487.539| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29170 Z= 0.127 Angle : 0.660 15.433 40610 Z= 0.354 Chirality : 0.042 0.224 4484 Planarity : 0.005 0.146 4146 Dihedral : 25.811 82.518 6262 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.78 % Allowed : 25.72 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2654 helix: 1.49 (0.14), residues: 1513 sheet: -0.87 (0.47), residues: 112 loop : -1.17 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 826 TYR 0.033 0.001 TYR F 549 PHE 0.040 0.001 PHE B 377 TRP 0.018 0.001 TRP A 719 HIS 0.008 0.001 HIS F 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (29151) covalent geometry : angle 0.65688 / 0.35 (40598) hydrogen bonds : bond 0.04279 / 2.79 ( 1482) hydrogen bonds : angle 3.71839 / 2.64 ( 4035) metal coordination : bond 0.00506 / 0.33 ( 19) metal coordination : angle 3.67129 / 2.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.94 seconds wall clock time: 77 minutes 23.04 seconds (4643.04 seconds total)