Starting phenix.real_space_refine on Mon Jun 23 19:09:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9d_37365/06_2025/8w9d_37365_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9d_37365/06_2025/8w9d_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_37365/06_2025/8w9d_37365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9d_37365/06_2025/8w9d_37365.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9d_37365/06_2025/8w9d_37365_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9d_37365/06_2025/8w9d_37365_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 14.53, per 1000 atoms: 0.52 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: 6.12 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 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: 12.19 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: 16.66 Time building geometry restraints manager: 7.37 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 2.850 ... (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: 1.510 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 76.810 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 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= 0.696 Angle : 1.158 37.221 40610 Z= 0.719 Chirality : 0.072 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 : 10.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.059 0.005 TRP E 301 HIS 0.009 0.001 HIS G 80 PHE 0.048 0.002 PHE E 387 TYR 0.063 0.002 TYR B 176 ARG 0.013 0.001 ARG A 917 Details of bonding type rmsd hydrogen bonds : bond 0.13165 ( 1482) hydrogen bonds : angle 5.23737 ( 4035) metal coordination : bond 0.28420 ( 19) metal coordination : angle 14.82780 ( 12) covalent geometry : bond 0.01031 (29151) covalent geometry : angle 1.12983 (40598) *********************** 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 : 2.801 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: 0.6941 (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: 0.4742 (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: 0.5852 (t) REVERT: A 1069 LEU cc_start: -0.1619 (OUTLIER) cc_final: -0.2657 (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: 0.5350 (t80) REVERT: E 105 ASP cc_start: -0.4256 (OUTLIER) cc_final: -0.4793 (t70) REVERT: E 318 THR cc_start: 0.4647 (p) cc_final: 0.4290 (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: 0.5079 (mt) REVERT: E 491 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6410 (p) REVERT: E 569 PHE cc_start: 0.3812 (t80) cc_final: 0.3255 (t80) REVERT: B 40 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3900 (tpt) REVERT: B 74 MET cc_start: 0.5258 (mtt) cc_final: 0.5056 (mtt) REVERT: C 364 VAL cc_start: 0.7964 (m) cc_final: 0.7621 (p) REVERT: D 217 THR cc_start: 0.2408 (OUTLIER) cc_final: 0.1761 (t) REVERT: D 325 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3274 (mp) REVERT: D 337 VAL cc_start: 0.6224 (OUTLIER) cc_final: 0.5569 (t) REVERT: D 345 THR cc_start: 0.6046 (OUTLIER) cc_final: 0.5759 (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: 0.7036 (p) REVERT: F 556 TYR cc_start: 0.4570 (t80) cc_final: 0.3804 (t80) REVERT: a 120 MET cc_start: 0.7471 (mtt) cc_final: 0.6944 (mtt) REVERT: b 80 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7155 (t) REVERT: b 88 TYR cc_start: 0.7865 (m-10) cc_final: 0.6764 (m-80) REVERT: d 87 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6814 (t) REVERT: G 22 MET cc_start: 0.0044 (mtm) cc_final: -0.1046 (tpp) outliers start: 201 outliers final: 26 residues processed: 751 average time/residue: 0.4507 time to fit residues: 512.4783 Evaluate side-chains 290 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 2.820 ------------------------------------------------------------------------------- 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 b residue 80 THR 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 245 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 138 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 930 HIS A1038 GLN A1216 ASN A1289 GLN E 342 ASN E 346 HIS E 376 ASN E 406 HIS 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 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 364 ASN C 330 HIS D 275 GLN D 277 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN D 358 GLN 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 c 38 ASN c 112 GLN d 49 HIS e 5 GLN e 76 GLN e 125 GLN g 73 ASN h 47 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.113551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.091363 restraints weight = 122281.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.091147 restraints weight = 93924.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.091442 restraints weight = 73503.060| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 2.002 29170 Z= 0.432 Angle : 0.732 13.266 40610 Z= 0.397 Chirality : 0.042 0.528 4484 Planarity : 0.005 0.100 4146 Dihedral : 25.991 82.560 6326 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.37 % Rotamer: Outliers : 4.69 % Allowed : 23.68 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2654 helix: 0.51 (0.13), residues: 1505 sheet: -0.93 (0.51), residues: 102 loop : -2.03 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 236 HIS 0.012 0.001 HIS A1252 PHE 0.043 0.002 PHE B 377 TYR 0.022 0.002 TYR C 306 ARG 0.007 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 1482) hydrogen bonds : angle 4.09005 ( 4035) metal coordination : bond 0.45950 ( 19) metal coordination : angle 6.59038 ( 12) covalent geometry : bond 0.00401 (29151) covalent geometry : angle 0.72300 (40598) *********************** 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 397 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 2.796 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 1004 ASN cc_start: 0.6730 (m-40) cc_final: 0.6155 (t0) REVERT: A 1068 ILE cc_start: 0.3447 (mt) cc_final: 0.3095 (tp) REVERT: A 1069 LEU cc_start: -0.2152 (OUTLIER) cc_final: -0.2642 (mt) REVERT: A 1294 MET cc_start: 0.4195 (ptt) cc_final: 0.3933 (ptp) REVERT: A 1300 MET cc_start: 0.4063 (mtt) cc_final: 0.3862 (mtt) REVERT: A 1325 LYS cc_start: -0.3562 (OUTLIER) cc_final: -0.4049 (tppt) REVERT: E 358 LYS cc_start: 0.6343 (mtmt) cc_final: 0.6067 (ttmt) REVERT: E 371 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: E 390 SER cc_start: 0.4203 (OUTLIER) cc_final: 0.3930 (t) REVERT: E 512 ILE cc_start: 0.4636 (OUTLIER) cc_final: 0.4370 (mm) REVERT: C 323 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7861 (tt) REVERT: D 296 MET cc_start: 0.7476 (tmm) cc_final: 0.7065 (tmm) REVERT: D 303 ARG cc_start: 0.3985 (mtm180) cc_final: 0.3487 (mtm180) REVERT: D 353 GLN cc_start: 0.8469 (tt0) cc_final: 0.8013 (mt0) REVERT: D 355 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6602 (mt) REVERT: D 362 PHE cc_start: 0.5848 (t80) cc_final: 0.5491 (t80) REVERT: b 44 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8279 (tttm) REVERT: d 62 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: d 89 ILE cc_start: 0.6743 (mm) cc_final: 0.6319 (mm) REVERT: f 37 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8821 (mt) REVERT: h 90 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7209 (p) outliers start: 113 outliers final: 46 residues processed: 373 average time/residue: 0.3889 time to fit residues: 233.8494 Evaluate side-chains 264 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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 691 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 861 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1250 VAL 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 280 LYS Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 386 LEU 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 40 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 355 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 96 CYS Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain b residue 50 ILE 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 62 MET 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 37 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 HIS A1289 GLN E 346 HIS E 499 ASN E 519 ASN E 521 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN F 332 ASN c 73 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN h 82 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.092663 restraints weight = 124267.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.091864 restraints weight = 112280.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.092030 restraints weight = 97430.750| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29170 Z= 0.147 Angle : 0.640 13.557 40610 Z= 0.350 Chirality : 0.039 0.319 4484 Planarity : 0.005 0.131 4146 Dihedral : 25.645 80.846 6276 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 3.32 % Allowed : 24.26 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2654 helix: 1.08 (0.13), residues: 1515 sheet: -0.70 (0.50), residues: 102 loop : -1.76 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 236 HIS 0.005 0.001 HIS A1252 PHE 0.027 0.002 PHE B 377 TYR 0.040 0.002 TYR A1286 ARG 0.011 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 1482) hydrogen bonds : angle 3.75151 ( 4035) metal coordination : bond 0.00889 ( 19) metal coordination : angle 4.92436 ( 12) covalent geometry : bond 0.00315 (29151) covalent geometry : angle 0.63421 (40598) *********************** 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 352 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 272 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LEU cc_start: 0.7616 (mt) cc_final: 0.7258 (tp) REVERT: A 800 LYS cc_start: 0.4588 (OUTLIER) cc_final: 0.4220 (mmmm) REVERT: A 941 LYS cc_start: 0.7479 (tttp) cc_final: 0.6973 (ptmt) REVERT: A 1004 ASN cc_start: 0.6806 (m-40) cc_final: 0.6240 (t0) REVERT: A 1068 ILE cc_start: 0.3468 (mt) cc_final: 0.3075 (tp) REVERT: A 1069 LEU cc_start: -0.2400 (OUTLIER) cc_final: -0.2677 (mt) REVERT: A 1300 MET cc_start: 0.4169 (mtt) cc_final: 0.3901 (mtt) REVERT: A 1325 LYS cc_start: -0.3801 (OUTLIER) cc_final: -0.4163 (tppt) REVERT: E 260 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.3240 (tt0) REVERT: E 371 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: E 512 ILE cc_start: 0.4189 (OUTLIER) cc_final: 0.3908 (mm) REVERT: E 516 ASN cc_start: 0.2607 (OUTLIER) cc_final: 0.1315 (t0) REVERT: B 53 MET cc_start: 0.6861 (mmt) cc_final: 0.6448 (mmm) REVERT: B 358 SER cc_start: 0.4418 (OUTLIER) cc_final: 0.4159 (t) REVERT: C 324 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.7287 (ttp80) REVERT: D 296 MET cc_start: 0.7635 (tmm) cc_final: 0.7345 (tmm) REVERT: D 353 GLN cc_start: 0.8589 (tt0) cc_final: 0.8052 (mt0) REVERT: D 355 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6679 (mt) REVERT: F 274 CYS cc_start: -0.0661 (t) cc_final: -0.1142 (p) REVERT: F 342 ASN cc_start: 0.5289 (m-40) cc_final: 0.4902 (m-40) REVERT: b 44 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8211 (tttm) REVERT: c 17 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7854 (mpp80) REVERT: c 73 ASN cc_start: 0.7377 (t160) cc_final: 0.7018 (t0) REVERT: f 50 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8272 (mm) REVERT: h 90 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.6816 (p) outliers start: 80 outliers final: 34 residues processed: 335 average time/residue: 0.3882 time to fit residues: 210.6800 Evaluate side-chains 259 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1199 VAL 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 260 GLU Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 SER 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 248 LEU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain F residue 286 CYS 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 b residue 50 ILE 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 114 VAL Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 287 optimal weight: 0.0970 chunk 190 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 77 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN E 268 GLN E 346 HIS E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN c 104 GLN g 38 ASN h 63 ASN h 82 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.092455 restraints weight = 123903.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.091956 restraints weight = 129524.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.092537 restraints weight = 103830.815| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29170 Z= 0.153 Angle : 0.631 10.569 40610 Z= 0.346 Chirality : 0.038 0.199 4484 Planarity : 0.005 0.129 4146 Dihedral : 25.498 81.423 6269 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.91 % Allowed : 23.14 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2654 helix: 1.38 (0.13), residues: 1510 sheet: -0.61 (0.49), residues: 102 loop : -1.51 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 775 HIS 0.005 0.001 HIS A1252 PHE 0.019 0.002 PHE F 326 TYR 0.037 0.002 TYR d 83 ARG 0.009 0.001 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1482) hydrogen bonds : angle 3.70550 ( 4035) metal coordination : bond 0.00703 ( 19) metal coordination : angle 3.78137 ( 12) covalent geometry : bond 0.00335 (29151) covalent geometry : angle 0.62778 (40598) *********************** 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 326 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 232 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 901 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6492 (mmmt) REVERT: A 956 LYS cc_start: 0.7714 (tttm) cc_final: 0.7351 (ptmm) REVERT: A 1004 ASN cc_start: 0.6782 (m-40) cc_final: 0.6205 (t0) REVERT: A 1207 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 1300 MET cc_start: 0.4229 (mtt) cc_final: 0.3998 (mtt) REVERT: E 175 MET cc_start: 0.3306 (pmm) cc_final: 0.2956 (pmm) REVERT: E 396 THR cc_start: 0.7822 (t) cc_final: 0.7571 (m) REVERT: E 407 ILE cc_start: 0.7668 (mt) cc_final: 0.7397 (mm) REVERT: E 512 ILE cc_start: 0.4512 (OUTLIER) cc_final: 0.4244 (mm) REVERT: E 516 ASN cc_start: 0.1908 (OUTLIER) cc_final: 0.1334 (t0) REVERT: C 324 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7263 (ttp80) REVERT: C 381 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6145 (ttm110) REVERT: D 296 MET cc_start: 0.7406 (tmm) cc_final: 0.7047 (tmm) REVERT: D 353 GLN cc_start: 0.8422 (tt0) cc_final: 0.7939 (mt0) REVERT: D 355 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6656 (mt) REVERT: D 363 LEU cc_start: 0.5610 (pp) cc_final: 0.5328 (pp) REVERT: F 274 CYS cc_start: -0.0893 (t) cc_final: -0.1183 (p) REVERT: F 332 ASN cc_start: 0.4962 (OUTLIER) cc_final: 0.4723 (t0) REVERT: F 342 ASN cc_start: 0.5292 (m-40) cc_final: 0.4972 (m-40) REVERT: b 44 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8258 (tttm) REVERT: c 17 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8054 (mpp80) REVERT: c 73 ASN cc_start: 0.7322 (t160) cc_final: 0.7103 (t0) REVERT: h 90 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.6942 (p) REVERT: G 22 MET cc_start: 0.1832 (tpp) cc_final: 0.1131 (tmm) outliers start: 94 outliers final: 49 residues processed: 308 average time/residue: 0.3787 time to fit residues: 191.7207 Evaluate side-chains 261 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 691 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS 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 1023 SER Chi-restraints excluded: chain A residue 1207 VAL 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 346 HIS Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 385 TYR 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 C residue 381 ARG 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 341 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain a residue 50 GLU 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 b residue 50 ILE 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 114 VAL Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain e residue 62 ILE Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 56 SER Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 113 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN E 519 ASN E 570 GLN B 31 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN D 275 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 104 GLN e 68 GLN h 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.108360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.088687 restraints weight = 125159.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.088340 restraints weight = 134817.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.088529 restraints weight = 111243.748| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29170 Z= 0.240 Angle : 0.739 10.031 40610 Z= 0.401 Chirality : 0.043 0.228 4484 Planarity : 0.006 0.142 4146 Dihedral : 25.983 83.907 6266 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 5.36 % Allowed : 22.68 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2654 helix: 0.89 (0.13), residues: 1523 sheet: -0.91 (0.48), residues: 97 loop : -1.61 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 464 HIS 0.037 0.002 HIS E 346 PHE 0.025 0.003 PHE a 78 TYR 0.022 0.002 TYR A1204 ARG 0.006 0.001 ARG c 88 Details of bonding type rmsd hydrogen bonds : bond 0.06152 ( 1482) hydrogen bonds : angle 4.11986 ( 4035) metal coordination : bond 0.01884 ( 19) metal coordination : angle 5.23822 ( 12) covalent geometry : bond 0.00539 (29151) covalent geometry : angle 0.73347 (40598) *********************** 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 338 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 209 time to evaluate : 2.741 Fit side-chains revert: symmetry clash REVERT: A 679 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5732 (ptpp) REVERT: A 841 MET cc_start: 0.3357 (pmm) cc_final: 0.3113 (mmm) REVERT: A 901 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6536 (mmmt) REVERT: A 956 LYS cc_start: 0.7767 (tttm) cc_final: 0.7351 (ttpp) REVERT: A 1004 ASN cc_start: 0.6877 (m-40) cc_final: 0.6078 (t0) REVERT: E 175 MET cc_start: 0.3294 (pmm) cc_final: 0.2918 (pmm) REVERT: E 503 GLN cc_start: 0.5998 (OUTLIER) cc_final: 0.5234 (tm-30) REVERT: E 562 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.5263 (pt0) REVERT: E 569 PHE cc_start: 0.3086 (OUTLIER) cc_final: 0.2432 (t80) REVERT: B 55 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.5278 (t80) REVERT: B 61 MET cc_start: 0.5714 (ppp) cc_final: 0.4950 (ppp) REVERT: B 239 ARG cc_start: 0.5664 (mtt90) cc_final: 0.4816 (mmt90) REVERT: C 324 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7226 (ttp80) REVERT: D 296 MET cc_start: 0.7656 (tmm) cc_final: 0.7230 (tmm) REVERT: D 324 ARG cc_start: 0.6435 (mmp-170) cc_final: 0.5838 (mmp-170) REVERT: D 355 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6505 (mt) REVERT: a 133 GLU cc_start: 0.5103 (mt-10) cc_final: 0.4800 (mt-10) REVERT: b 44 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8656 (tmtt) REVERT: d 62 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7349 (mpp) REVERT: d 73 ILE cc_start: 0.8583 (mm) cc_final: 0.8158 (mt) REVERT: h 90 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7165 (p) REVERT: h 93 GLU cc_start: 0.7992 (mp0) cc_final: 0.7694 (mp0) REVERT: G 22 MET cc_start: 0.1137 (tpp) cc_final: 0.0561 (tmm) outliers start: 129 outliers final: 69 residues processed: 311 average time/residue: 0.3782 time to fit residues: 191.8298 Evaluate side-chains 259 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 2.777 ------------------------------------------------------------------------------- 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 790 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS 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 1023 SER 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 111 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain E residue 569 PHE Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 231 VAL 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 C residue 381 ARG 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 293 LEU 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 D residue 388 VAL Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain a residue 46 VAL 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 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 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 86 SER 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 g residue 16 THR Chi-restraints excluded: chain g residue 40 SER 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 56 SER Chi-restraints excluded: chain h residue 63 ASN 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 152 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 88 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 0.0670 chunk 182 optimal weight: 7.9990 overall best weight: 2.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS E 516 ASN E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN c 73 ASN e 108 ASN g 73 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.109894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.091646 restraints weight = 124851.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.091125 restraints weight = 141871.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091581 restraints weight = 118201.892| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.650 29170 Z= 0.197 Angle : 0.631 10.704 40610 Z= 0.346 Chirality : 0.038 0.228 4484 Planarity : 0.005 0.137 4146 Dihedral : 25.626 82.061 6264 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 3.70 % Allowed : 24.18 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2654 helix: 1.29 (0.13), residues: 1514 sheet: -0.80 (0.51), residues: 83 loop : -1.43 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 301 HIS 0.007 0.001 HIS B 38 PHE 0.033 0.002 PHE A1021 TYR 0.025 0.001 TYR d 83 ARG 0.006 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1482) hydrogen bonds : angle 3.77367 ( 4035) metal coordination : bond 0.14937 ( 19) metal coordination : angle 3.61479 ( 12) covalent geometry : bond 0.00328 (29151) covalent geometry : angle 0.62821 (40598) *********************** 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 313 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 224 time to evaluate : 2.789 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5757 (m-80) REVERT: A 841 MET cc_start: 0.3767 (pmm) cc_final: 0.3110 (mmm) REVERT: A 901 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6498 (mmmt) REVERT: A 956 LYS cc_start: 0.7698 (tttm) cc_final: 0.7265 (ptmm) REVERT: A 1004 ASN cc_start: 0.6779 (m-40) cc_final: 0.6073 (t0) REVERT: A 1220 GLU cc_start: 0.6799 (mm-30) cc_final: 0.5855 (tp30) REVERT: E 352 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5428 (pp30) REVERT: E 503 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.4894 (tm-30) REVERT: B 55 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.5115 (t80) REVERT: B 61 MET cc_start: 0.5697 (ppp) cc_final: 0.5052 (ppp) REVERT: C 324 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7098 (ttp80) REVERT: C 381 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6177 (ttm110) REVERT: D 296 MET cc_start: 0.7514 (tmm) cc_final: 0.7200 (tmm) REVERT: D 324 ARG cc_start: 0.6299 (mmp-170) cc_final: 0.5726 (mmp-170) REVERT: D 363 LEU cc_start: 0.5931 (pp) cc_final: 0.5665 (pp) REVERT: a 90 MET cc_start: 0.6874 (mmm) cc_final: 0.6558 (mmt) REVERT: b 44 LYS cc_start: 0.8786 (tmtt) cc_final: 0.8561 (tmtt) REVERT: c 43 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7944 (t) REVERT: d 62 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7074 (mmt) REVERT: f 84 MET cc_start: 0.7603 (tpt) cc_final: 0.7398 (mmm) REVERT: G 22 MET cc_start: 0.0617 (tpp) cc_final: 0.0057 (tmm) outliers start: 89 outliers final: 53 residues processed: 288 average time/residue: 0.3557 time to fit residues: 170.2805 Evaluate side-chains 255 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 901 LYS 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 1023 SER Chi-restraints excluded: chain A residue 1138 LEU 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 260 GLU Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 366 THR 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 498 ILE Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 325 GLU 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 C residue 381 ARG Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 388 VAL 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 96 CYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL 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 73 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 244 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS F 342 ASN g 38 ASN g 73 ASN h 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.108296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.089884 restraints weight = 125981.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.089280 restraints weight = 152698.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.089699 restraints weight = 122706.777| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29170 Z= 0.197 Angle : 0.680 10.858 40610 Z= 0.372 Chirality : 0.040 0.186 4484 Planarity : 0.005 0.142 4146 Dihedral : 25.751 86.594 6264 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 4.20 % Allowed : 24.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2654 helix: 1.12 (0.13), residues: 1520 sheet: -1.16 (0.52), residues: 79 loop : -1.42 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 788 HIS 0.008 0.001 HIS B 38 PHE 0.020 0.002 PHE F 326 TYR 0.020 0.002 TYR F 549 ARG 0.005 0.001 ARG c 88 Details of bonding type rmsd hydrogen bonds : bond 0.05408 ( 1482) hydrogen bonds : angle 3.93951 ( 4035) metal coordination : bond 0.01230 ( 19) metal coordination : angle 4.84734 ( 12) covalent geometry : bond 0.00440 (29151) covalent geometry : angle 0.67479 (40598) *********************** 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 305 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 204 time to evaluate : 2.582 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: A 841 MET cc_start: 0.4197 (pmm) cc_final: 0.3106 (mmm) REVERT: A 956 LYS cc_start: 0.7692 (tttm) cc_final: 0.7300 (ttpp) REVERT: A 1004 ASN cc_start: 0.6854 (m-40) cc_final: 0.6024 (t0) REVERT: E 352 GLN cc_start: 0.5900 (OUTLIER) cc_final: 0.5533 (pp30) REVERT: E 569 PHE cc_start: 0.3165 (OUTLIER) cc_final: 0.2466 (t80) REVERT: B 55 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.5074 (t80) REVERT: B 96 MET cc_start: 0.7827 (ttm) cc_final: 0.7626 (ttm) REVERT: C 324 ARG cc_start: 0.7579 (ptm-80) cc_final: 0.7221 (ttp80) REVERT: D 251 ASP cc_start: 0.3140 (OUTLIER) cc_final: 0.2264 (m-30) REVERT: D 296 MET cc_start: 0.7626 (tmm) cc_final: 0.7198 (tmm) REVERT: D 324 ARG cc_start: 0.6374 (mmp-170) cc_final: 0.6092 (mmp-170) REVERT: F 549 TYR cc_start: 0.4649 (m-80) cc_final: 0.4424 (m-80) REVERT: c 43 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8127 (t) REVERT: d 73 ILE cc_start: 0.8728 (mm) cc_final: 0.8223 (mt) REVERT: G 22 MET cc_start: 0.0420 (tpp) cc_final: 0.0019 (tmm) outliers start: 101 outliers final: 70 residues processed: 280 average time/residue: 0.3585 time to fit residues: 165.6848 Evaluate side-chains 262 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 710 LEU 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 862 ILE 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 1023 SER Chi-restraints excluded: chain A residue 1138 LEU 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 111 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 352 GLN 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 452 VAL Chi-restraints excluded: chain E residue 569 PHE Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 325 GLU 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 306 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 388 VAL 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 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 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 264 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 274 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN g 73 ASN h 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.109605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.090429 restraints weight = 125136.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.090380 restraints weight = 125307.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.090703 restraints weight = 100559.378| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29170 Z= 0.148 Angle : 0.634 10.105 40610 Z= 0.346 Chirality : 0.038 0.176 4484 Planarity : 0.005 0.142 4146 Dihedral : 25.547 84.695 6264 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 3.66 % Allowed : 24.76 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2654 helix: 1.41 (0.13), residues: 1513 sheet: -0.92 (0.54), residues: 79 loop : -1.32 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 365 HIS 0.007 0.001 HIS B 38 PHE 0.041 0.001 PHE F 552 TYR 0.029 0.001 TYR d 83 ARG 0.007 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 1482) hydrogen bonds : angle 3.73624 ( 4035) metal coordination : bond 0.00702 ( 19) metal coordination : angle 3.98221 ( 12) covalent geometry : bond 0.00321 (29151) covalent geometry : angle 0.62989 (40598) *********************** 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 302 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 214 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: A 841 MET cc_start: 0.3771 (pmm) cc_final: 0.3234 (mmm) REVERT: A 956 LYS cc_start: 0.7725 (tttm) cc_final: 0.7284 (ptmm) REVERT: A 1004 ASN cc_start: 0.6667 (m-40) cc_final: 0.5940 (t0) REVERT: A 1220 GLU cc_start: 0.6955 (mm-30) cc_final: 0.5880 (tp30) REVERT: E 333 VAL cc_start: 0.5890 (OUTLIER) cc_final: 0.5615 (m) REVERT: B 55 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.5179 (t80) REVERT: C 324 ARG cc_start: 0.7515 (ptm-80) cc_final: 0.7198 (ttp80) REVERT: C 381 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6201 (ttm110) REVERT: D 251 ASP cc_start: 0.3116 (OUTLIER) cc_final: 0.2486 (m-30) REVERT: D 256 MET cc_start: 0.4339 (tmm) cc_final: 0.4025 (tpt) REVERT: D 296 MET cc_start: 0.7620 (tmm) cc_final: 0.7204 (tmm) REVERT: D 324 ARG cc_start: 0.6373 (mmp-170) cc_final: 0.6100 (mmp-170) REVERT: D 365 TRP cc_start: 0.4303 (OUTLIER) cc_final: 0.3909 (t-100) REVERT: a 90 MET cc_start: 0.7077 (mmm) cc_final: 0.6729 (mmt) REVERT: b 44 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8221 (tttm) REVERT: b 92 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7297 (ptm-80) REVERT: c 43 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8061 (t) REVERT: d 62 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7192 (mmt) REVERT: e 5 GLN cc_start: 0.2841 (mt0) cc_final: 0.2477 (mt0) REVERT: f 37 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8820 (mt) REVERT: G 22 MET cc_start: 0.0539 (tpp) cc_final: 0.0183 (tmm) outliers start: 88 outliers final: 62 residues processed: 283 average time/residue: 0.3673 time to fit residues: 172.3598 Evaluate side-chains 265 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1138 LEU 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 181 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 333 VAL 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 402 ASN Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 325 GLU 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 C residue 381 ARG Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain D residue 388 VAL 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 b residue 92 ARG 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 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 16 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 63 ASN 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 132 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 8 optimal weight: 0.0270 chunk 251 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN E 352 GLN E 402 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN g 73 ASN h 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.108357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.088578 restraints weight = 125326.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.088417 restraints weight = 116397.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.088637 restraints weight = 94378.422| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29170 Z= 0.189 Angle : 0.676 15.499 40610 Z= 0.367 Chirality : 0.040 0.176 4484 Planarity : 0.005 0.149 4146 Dihedral : 25.642 87.784 6263 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 3.41 % Allowed : 24.84 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2654 helix: 1.28 (0.13), residues: 1508 sheet: -1.01 (0.55), residues: 79 loop : -1.36 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 788 HIS 0.007 0.001 HIS B 38 PHE 0.023 0.002 PHE F 552 TYR 0.041 0.002 TYR d 83 ARG 0.006 0.001 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 1482) hydrogen bonds : angle 3.85269 ( 4035) metal coordination : bond 0.01143 ( 19) metal coordination : angle 4.56389 ( 12) covalent geometry : bond 0.00419 (29151) covalent geometry : angle 0.67187 (40598) *********************** 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 275 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 193 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 841 MET cc_start: 0.4280 (pmm) cc_final: 0.3156 (mmm) REVERT: A 956 LYS cc_start: 0.7782 (tttm) cc_final: 0.7342 (ttpp) REVERT: A 1004 ASN cc_start: 0.6761 (m-40) cc_final: 0.5969 (t0) REVERT: E 333 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5179 (m) REVERT: B 47 MET cc_start: 0.6435 (mtt) cc_final: 0.6135 (mtt) REVERT: B 55 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5277 (t80) REVERT: B 259 MET cc_start: 0.7804 (tmm) cc_final: 0.7571 (tmm) REVERT: C 324 ARG cc_start: 0.7603 (ptm-80) cc_final: 0.7272 (ttp80) REVERT: D 251 ASP cc_start: 0.3043 (OUTLIER) cc_final: 0.2692 (m-30) REVERT: D 256 MET cc_start: 0.4580 (tmm) cc_final: 0.4282 (tpt) REVERT: D 296 MET cc_start: 0.7733 (tmm) cc_final: 0.7286 (tmm) REVERT: D 324 ARG cc_start: 0.6416 (mmp-170) cc_final: 0.6179 (mmp-170) REVERT: D 365 TRP cc_start: 0.4306 (OUTLIER) cc_final: 0.3986 (t-100) REVERT: b 44 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8162 (tttm) REVERT: c 43 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8084 (t) REVERT: d 62 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7184 (mmt) REVERT: e 5 GLN cc_start: 0.2986 (mt0) cc_final: 0.2595 (mt0) REVERT: f 37 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8814 (mt) REVERT: G 22 MET cc_start: 0.0636 (tpp) cc_final: 0.0371 (tmm) outliers start: 82 outliers final: 68 residues processed: 257 average time/residue: 0.3509 time to fit residues: 150.1224 Evaluate side-chains 262 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1138 LEU 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 111 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 333 VAL 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 402 ASN Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 325 GLU 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 C residue 381 ARG Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain D residue 388 VAL 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 42 TYR Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 63 ASN 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 168 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 205 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN E 259 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN f 75 HIS g 38 ASN g 73 ASN h 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.107223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.088615 restraints weight = 127093.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.088328 restraints weight = 137506.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.088566 restraints weight = 110142.137| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.7348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29170 Z= 0.228 Angle : 0.733 15.211 40610 Z= 0.394 Chirality : 0.042 0.207 4484 Planarity : 0.006 0.154 4146 Dihedral : 25.867 88.956 6263 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 3.61 % Allowed : 24.51 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2654 helix: 1.01 (0.13), residues: 1498 sheet: -0.96 (0.53), residues: 89 loop : -1.50 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 788 HIS 0.008 0.002 HIS B 38 PHE 0.024 0.002 PHE F 552 TYR 0.037 0.002 TYR F 549 ARG 0.006 0.001 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.05819 ( 1482) hydrogen bonds : angle 4.06150 ( 4035) metal coordination : bond 0.01569 ( 19) metal coordination : angle 7.39366 ( 12) covalent geometry : bond 0.00515 (29151) covalent geometry : angle 0.72151 (40598) ********************** 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 276 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 189 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.4449 (pmm) cc_final: 0.3326 (mmm) REVERT: A 956 LYS cc_start: 0.7774 (tttm) cc_final: 0.7311 (ttpp) REVERT: A 1004 ASN cc_start: 0.6676 (m-40) cc_final: 0.5738 (t0) REVERT: E 569 PHE cc_start: 0.3174 (OUTLIER) cc_final: 0.2446 (t80) REVERT: B 55 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.4850 (t80) REVERT: C 324 ARG cc_start: 0.7524 (ptm-80) cc_final: 0.7191 (ttp80) REVERT: D 296 MET cc_start: 0.7701 (tmm) cc_final: 0.7277 (tmm) REVERT: D 365 TRP cc_start: 0.4142 (OUTLIER) cc_final: 0.3772 (t-100) REVERT: b 44 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8218 (tttm) REVERT: b 92 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7319 (ptm-80) REVERT: c 43 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8164 (t) REVERT: d 62 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7194 (mmt) REVERT: e 39 HIS cc_start: 0.7117 (t-90) cc_final: 0.6666 (t70) REVERT: G 22 MET cc_start: 0.0431 (tpp) cc_final: 0.0189 (tmm) outliers start: 87 outliers final: 69 residues processed: 255 average time/residue: 0.3749 time to fit residues: 160.6147 Evaluate side-chains 252 residues out of total 2414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1138 LEU 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 111 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 404 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 569 PHE Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 325 GLU 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 C residue 381 ARG Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 365 TRP Chi-restraints excluded: chain D residue 388 VAL 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 b residue 92 ARG 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 61 ILE Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 62 ILE Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 74 LYS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 114 VAL 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 249 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN c 38 ASN g 73 ASN h 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.089500 restraints weight = 127014.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089194 restraints weight = 144443.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.089550 restraints weight = 119747.069| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29170 Z= 0.194 Angle : 0.692 14.770 40610 Z= 0.375 Chirality : 0.040 0.194 4484 Planarity : 0.005 0.152 4146 Dihedral : 25.776 89.566 6263 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 3.45 % Allowed : 24.55 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2654 helix: 1.10 (0.13), residues: 1498 sheet: -0.93 (0.53), residues: 89 loop : -1.51 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 788 HIS 0.006 0.001 HIS E 469 PHE 0.022 0.002 PHE E 387 TYR 0.042 0.002 TYR d 83 ARG 0.005 0.001 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 1482) hydrogen bonds : angle 3.95271 ( 4035) metal coordination : bond 0.01244 ( 19) metal coordination : angle 6.05879 ( 12) covalent geometry : bond 0.00433 (29151) covalent geometry : angle 0.68423 (40598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8703.17 seconds wall clock time: 152 minutes 22.93 seconds (9142.93 seconds total)