Starting phenix.real_space_refine on Mon May 26 19:54:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449.map" model { file = "/net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tof_41449/05_2025/8tof_41449_neut.cif" } resolution = 2.8 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 352 5.49 5 S 106 5.16 5 C 17364 2.51 5 N 5145 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29102 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4572 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 12, 'TRANS': 532} Chain breaks: 2 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 18, 'TRANS': 366} Chain: "D" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2356 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Chain: "E" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2080 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 9, 'TRANS': 243} Chain breaks: 2 Chain: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain breaks: 1 Chain: "G" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3010 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 347} Chain breaks: 5 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 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: "N" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3623 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "T" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3593 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "a" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 836 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "c" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 836 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 39 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13483 SG CYS G 263 62.286 92.071 104.064 1.00130.04 S ATOM 13500 SG CYS G 266 63.824 89.998 106.938 1.00119.58 S ATOM 13653 SG CYS G 286 60.707 92.300 107.591 1.00121.45 S ATOM 14713 SG CYS G 417 84.879 61.141 134.087 1.00108.79 S ATOM 14740 SG CYS G 420 85.278 57.617 135.012 1.00 91.61 S ATOM 14996 SG CYS G 451 81.929 59.290 135.694 1.00103.95 S ATOM 14901 SG CYS G 440 84.803 72.069 128.218 1.00106.26 S ATOM 14927 SG CYS G 443 87.496 72.672 130.949 1.00102.20 S ATOM 15116 SG CYS G 466 84.559 70.340 131.371 1.00116.46 S ATOM 13564 SG CYS G 275 57.244 98.911 94.446 1.00165.73 S ATOM 13585 SG CYS G 278 60.521 98.388 94.954 1.00166.34 S ATOM 13788 SG CYS G 303 60.415 101.428 96.372 1.00168.52 S Time building chain proxies: 16.75, per 1000 atoms: 0.58 Number of scatterers: 29102 At special positions: 0 Unit cell: (147.138, 160.29, 187.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 106 16.00 P 352 15.00 O 6130 8.00 N 5145 7.00 C 17364 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: 7.19 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" ND1 HIS G 283 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 263 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 266 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 286 " pdb=" ZN G 702 " pdb="ZN ZN G 702 " - pdb=" ND1 HIS G 448 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 420 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 417 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 451 " pdb=" ZN G 703 " pdb="ZN ZN G 703 " - pdb=" NE2 HIS G 469 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 466 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 440 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 443 " pdb=" ZN G 704 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 278 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 275 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 303 " Number of angles added : 9 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 21 sheets defined 59.2% alpha, 5.8% beta 169 base pairs and 303 stacking pairs defined. Time for finding SS restraints: 11.79 Creating SS restraints... Processing helix chain 'A' and resid 664 through 676 removed outlier: 4.005A pdb=" N PHE A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.547A pdb=" N TYR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 710 removed outlier: 3.527A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.664A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.608A pdb=" N SER A 790 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 791 " --> pdb=" O TRP A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.523A pdb=" N SER A 823 " --> pdb=" O PHE A 819 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.171A pdb=" N GLY A 856 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.596A pdb=" N HIS A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 928 removed outlier: 3.806A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.532A pdb=" N LEU A 933 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 929 through 934' Processing helix chain 'A' and resid 937 through 943 Processing helix chain 'A' and resid 944 through 965 removed outlier: 3.598A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 999 Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.697A pdb=" N ARG A1009 " --> pdb=" O PRO A1005 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1039 removed outlier: 3.752A pdb=" N ASN A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 3.591A pdb=" N PHE A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1184 removed outlier: 4.053A pdb=" N ASP A1183 " --> pdb=" O THR A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.573A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1220 through 1230 removed outlier: 3.730A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1242 through 1258 Processing helix chain 'A' and resid 1260 through 1274 Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.515A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.939A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.563A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.726A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 301 removed outlier: 3.924A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 330 removed outlier: 3.762A pdb=" N THR B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.245A pdb=" N ASN D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.594A pdb=" N TRP D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 101 through 131 Processing helix chain 'D' and resid 225 through 240 removed outlier: 3.776A pdb=" N THR D 240 " --> pdb=" O TRP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 270 through 297 removed outlier: 3.997A pdb=" N SER D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 279 " --> pdb=" O GLN D 275 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 317 removed outlier: 4.463A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.666A 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 391 through 399 removed outlier: 3.727A pdb=" N VAL D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.153A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 101 through 131 Processing helix chain 'E' and resid 225 through 241 Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.559A pdb=" N SER E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 297 removed outlier: 6.237A pdb=" N GLY E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 317 removed outlier: 4.319A pdb=" N GLN E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 327 through 344 removed outlier: 3.554A pdb=" N LEU E 331 " --> pdb=" O GLY E 327 " (cutoff:3.500A) Proline residue: E 339 - end of helix Processing helix chain 'E' and resid 348 through 369 Processing helix chain 'E' and resid 369 through 375 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 346 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 292 through 296 removed outlier: 4.093A pdb=" N LEU G 296 " --> pdb=" O PRO G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 315 through 330 removed outlier: 3.618A pdb=" N LEU G 319 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 5.618A pdb=" N ILE G 335 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 344 removed outlier: 3.645A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 359 removed outlier: 3.723A pdb=" N LYS G 358 " --> pdb=" O PRO G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 387 Processing helix chain 'G' and resid 393 through 397 removed outlier: 3.597A pdb=" N THR G 396 " --> pdb=" O GLN G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 434 Processing helix chain 'G' and resid 544 through 565 removed outlier: 3.611A pdb=" N LYS G 548 " --> pdb=" O GLU G 544 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.569A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.428A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.509A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.693A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE e 78 " --> pdb=" O ILE e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.452A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 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 977 through 978 removed outlier: 3.796A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 237 removed outlier: 7.681A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 63 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER G 179 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG B 65 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 39 removed outlier: 6.455A pdb=" N PHE D 78 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 90 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.670A pdb=" N LEU D 21 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS D 18 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 23 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.469A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AA9, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB1, first strand: chain 'G' and resid 437 through 439 Processing sheet with id=AB2, first strand: chain 'G' and resid 476 through 477 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.814A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.248A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (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 Processing sheet with id=AB8, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.939A 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: 7.299A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (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 1141 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 169 basepair parallelities 303 stacking parallelities Total time for adding SS restraints: 17.57 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.24: 3049 1.24 - 1.58: 26494 1.58 - 1.92: 864 1.92 - 2.27: 0 2.27 - 2.61: 1 Bond restraints: 30408 Sorted by residual: bond pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " ideal model delta sigma weight residual 1.492 2.612 -1.120 5.00e-02 4.00e+02 5.02e+02 bond pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sigma weight residual 1.503 0.894 0.609 3.40e-02 8.65e+02 3.20e+02 bond pdb=" CG PRO E 322 " pdb=" CD PRO E 322 " ideal model delta sigma weight residual 1.503 1.017 0.486 3.40e-02 8.65e+02 2.04e+02 bond pdb=" N ML3 a 36 " pdb=" CA ML3 a 36 " ideal model delta sigma weight residual 1.458 1.264 0.194 1.90e-02 2.77e+03 1.04e+02 bond pdb=" N ML3 e 36 " pdb=" CA ML3 e 36 " ideal model delta sigma weight residual 1.458 1.265 0.193 1.90e-02 2.77e+03 1.03e+02 ... (remaining 30403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.52: 42547 19.52 - 39.04: 2 39.04 - 58.55: 0 58.55 - 78.07: 0 78.07 - 97.59: 1 Bond angle restraints: 42550 Sorted by residual: angle pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sigma weight residual 106.10 8.51 97.59 3.20e+00 9.77e-02 9.30e+02 angle pdb=" N PRO E 322 " pdb=" CD PRO E 322 " pdb=" CG PRO E 322 " ideal model delta sigma weight residual 103.20 72.21 30.99 1.50e+00 4.44e-01 4.27e+02 angle pdb=" CA PRO E 322 " pdb=" CB PRO E 322 " pdb=" CG PRO E 322 " ideal model delta sigma weight residual 104.50 73.46 31.04 1.90e+00 2.77e-01 2.67e+02 angle pdb=" N PRO F 279 " pdb=" CA PRO F 279 " pdb=" CB PRO F 279 " ideal model delta sigma weight residual 103.48 90.77 12.71 1.00e+00 1.00e+00 1.62e+02 angle pdb=" N PRO E 322 " pdb=" CA PRO E 322 " pdb=" CB PRO E 322 " ideal model delta sigma weight residual 103.25 92.43 10.82 1.05e+00 9.07e-01 1.06e+02 ... (remaining 42545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 15038 33.41 - 66.83: 2308 66.83 - 100.24: 62 100.24 - 133.65: 5 133.65 - 167.07: 4 Dihedral angle restraints: 17417 sinusoidal: 9498 harmonic: 7919 Sorted by residual: dihedral pdb=" CA LEU E 248 " pdb=" C LEU E 248 " pdb=" N PRO E 249 " pdb=" CA PRO E 249 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA LYS A 760 " pdb=" C LYS A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO F 279 " pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sinusoidal sigma weight residual 38.00 152.70 -114.70 1 2.00e+01 2.50e-03 3.40e+01 ... (remaining 17414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4518 0.098 - 0.195: 181 0.195 - 0.293: 1 0.293 - 0.391: 2 0.391 - 0.488: 1 Chirality restraints: 4703 Sorted by residual: chirality pdb=" CA ML3 a 36 " pdb=" N ML3 a 36 " pdb=" C ML3 a 36 " pdb=" CB ML3 a 36 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ML3 e 36 " pdb=" N ML3 e 36 " pdb=" C ML3 e 36 " pdb=" CB ML3 e 36 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA PRO F 279 " pdb=" N PRO F 279 " pdb=" C PRO F 279 " pdb=" CB PRO F 279 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 4700 not shown) Planarity restraints: 4180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 507 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO G 508 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO G 508 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 508 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 402 " 0.084 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 403 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO G 403 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 403 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 966 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP A 966 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 966 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 966 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 966 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 966 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 966 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 966 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 966 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 966 " 0.008 2.00e-02 2.50e+03 ... (remaining 4177 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 160 2.44 - 3.06: 19267 3.06 - 3.67: 48621 3.67 - 4.29: 73673 4.29 - 4.90: 112402 Nonbonded interactions: 254123 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 1.828 2.230 nonbonded pdb=" C2 DG N 38 " pdb=" N2 DG T -37 " model vdw 1.904 3.340 nonbonded pdb=" O2 DT N 9 " pdb=" NH2 ARG e 40 " model vdw 1.922 3.120 nonbonded pdb=" OG SER E 313 " pdb=" O LYS E 318 " model vdw 1.963 3.040 nonbonded pdb=" C2 DA N 59 " pdb=" N2 DG T -58 " model vdw 2.010 3.420 ... (remaining 254118 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 'D' and (resid 10 through 40 or resid 67 through 376)) selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 82.740 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.010 1.120 30424 Z= 0.376 Angle : 1.003 97.589 42559 Z= 0.560 Chirality : 0.044 0.488 4703 Planarity : 0.005 0.135 4180 Dihedral : 24.373 167.067 12293 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.58 % Favored : 92.97 % Rotamer: Outliers : 3.09 % Allowed : 26.11 % Favored : 70.80 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2631 helix: 1.18 (0.14), residues: 1435 sheet: -2.14 (0.48), residues: 114 loop : -1.24 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 236 HIS 0.006 0.001 HIS e 39 PHE 0.033 0.002 PHE E 362 TYR 0.018 0.002 TYR B 347 ARG 0.029 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.16800 ( 1564) hydrogen bonds : angle 5.92537 ( 4158) metal coordination : bond 0.09551 ( 16) metal coordination : angle 4.19641 ( 9) covalent geometry : bond 0.01020 (30408) covalent geometry : angle 1.00169 (42550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 302 time to evaluate : 2.566 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 1291 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6760 (tpt170) REVERT: B 220 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 78 PHE cc_start: 0.8227 (t80) cc_final: 0.7993 (t80) REVERT: G 552 PHE cc_start: 0.8263 (t80) cc_final: 0.8047 (t80) REVERT: a 56 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8855 (ttpp) REVERT: g 90 ASP cc_start: 0.8695 (t0) cc_final: 0.8398 (t0) outliers start: 74 outliers final: 54 residues processed: 365 average time/residue: 1.5407 time to fit residues: 653.6625 Evaluate side-chains 329 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 322 PRO Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain h residue 44 GLN Chi-restraints excluded: chain h residue 83 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 HIS A1150 HIS A1252 HIS B 43 HIS B 76 GLN B 341 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN G 541 GLN a 39 HIS b 75 HIS d 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080777 restraints weight = 59979.383| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.50 r_work: 0.3087 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30424 Z= 0.227 Angle : 0.661 13.260 42559 Z= 0.366 Chirality : 0.040 0.202 4703 Planarity : 0.005 0.085 4180 Dihedral : 26.951 166.161 6888 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.12 % Favored : 93.42 % Rotamer: Outliers : 4.80 % Allowed : 22.77 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2631 helix: 1.43 (0.14), residues: 1454 sheet: -2.47 (0.44), residues: 110 loop : -1.12 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 236 HIS 0.006 0.001 HIS a 39 PHE 0.020 0.002 PHE E 362 TYR 0.022 0.002 TYR B 347 ARG 0.009 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 1564) hydrogen bonds : angle 4.09180 ( 4158) metal coordination : bond 0.01491 ( 16) metal coordination : angle 5.19427 ( 9) covalent geometry : bond 0.00516 (30408) covalent geometry : angle 0.65690 (42550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 311 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8603 (t60) cc_final: 0.8247 (t60) REVERT: A 775 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6315 (t-100) REVERT: A 978 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: A 1156 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 1257 MET cc_start: 0.8299 (ptp) cc_final: 0.8069 (ptp) REVERT: A 1258 THR cc_start: 0.8698 (t) cc_final: 0.8424 (p) REVERT: B 220 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7428 (tm-30) REVERT: D 22 MET cc_start: 0.1572 (mmp) cc_final: 0.1089 (mmt) REVERT: D 77 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6603 (m-10) REVERT: D 78 PHE cc_start: 0.8316 (t80) cc_final: 0.8086 (t80) REVERT: D 237 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.4203 (mm-30) REVERT: D 310 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6266 (tp) REVERT: E 335 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6627 (mp) REVERT: E 373 TYR cc_start: 0.7574 (m-10) cc_final: 0.6844 (m-80) REVERT: F 333 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7883 (p) REVERT: G 175 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7205 (ptp) REVERT: G 305 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: G 377 ASP cc_start: 0.8399 (m-30) cc_final: 0.8122 (m-30) REVERT: G 552 PHE cc_start: 0.8599 (t80) cc_final: 0.8281 (t80) REVERT: G 553 ASP cc_start: 0.9119 (p0) cc_final: 0.8590 (m-30) REVERT: a 59 GLU cc_start: 0.8479 (pm20) cc_final: 0.8167 (pm20) REVERT: c 64 GLU cc_start: 0.8496 (tp30) cc_final: 0.8085 (tt0) REVERT: d 54 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8483 (mmtt) REVERT: f 92 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8779 (ttp80) REVERT: h 31 LYS cc_start: 0.8303 (mptp) cc_final: 0.8016 (mptp) outliers start: 115 outliers final: 43 residues processed: 396 average time/residue: 1.3911 time to fit residues: 643.7089 Evaluate side-chains 327 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 279 PRO Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 113 SER Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 135 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 ASN D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.125364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083339 restraints weight = 60291.353| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.49 r_work: 0.3146 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30424 Z= 0.156 Angle : 0.612 9.424 42559 Z= 0.339 Chirality : 0.037 0.209 4703 Planarity : 0.004 0.071 4180 Dihedral : 26.656 164.615 6819 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.59 % Favored : 93.99 % Rotamer: Outliers : 4.59 % Allowed : 22.35 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2631 helix: 1.68 (0.14), residues: 1459 sheet: -2.20 (0.45), residues: 109 loop : -0.98 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.005 0.001 HIS B 49 PHE 0.026 0.001 PHE A 668 TYR 0.022 0.001 TYR E 281 ARG 0.012 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1564) hydrogen bonds : angle 3.78928 ( 4158) metal coordination : bond 0.00734 ( 16) metal coordination : angle 3.69859 ( 9) covalent geometry : bond 0.00340 (30408) covalent geometry : angle 0.60981 (42550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 322 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 THR cc_start: 0.8976 (t) cc_final: 0.8759 (p) REVERT: A 719 TRP cc_start: 0.8638 (t60) cc_final: 0.8117 (t60) REVERT: A 722 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8760 (p0) REVERT: A 775 TRP cc_start: 0.6938 (OUTLIER) cc_final: 0.6279 (t-100) REVERT: A 780 ASP cc_start: 0.8414 (t0) cc_final: 0.8174 (m-30) REVERT: A 805 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7893 (mp0) REVERT: A 845 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: A 949 ILE cc_start: 0.8954 (mt) cc_final: 0.8708 (pp) REVERT: A 978 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: A 1156 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 1258 THR cc_start: 0.8582 (t) cc_final: 0.8364 (p) REVERT: A 1295 SER cc_start: 0.8705 (m) cc_final: 0.8288 (p) REVERT: B 76 GLN cc_start: 0.8882 (mt0) cc_final: 0.8616 (mt0) REVERT: B 220 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 18 HIS cc_start: 0.5118 (OUTLIER) cc_final: 0.4611 (m90) REVERT: D 22 MET cc_start: 0.1375 (mmp) cc_final: 0.1074 (mmt) REVERT: D 77 PHE cc_start: 0.7584 (m-80) cc_final: 0.6635 (m-80) REVERT: D 78 PHE cc_start: 0.8350 (t80) cc_final: 0.8091 (t80) REVERT: D 237 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.3924 (mm-30) REVERT: D 310 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6313 (tp) REVERT: D 320 LEU cc_start: 0.7667 (tp) cc_final: 0.6927 (tp) REVERT: E 23 TYR cc_start: 0.6463 (m-80) cc_final: 0.5851 (m-80) REVERT: E 38 TYR cc_start: 0.6147 (p90) cc_final: 0.5846 (p90) REVERT: E 263 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7222 (t-170) REVERT: E 335 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6742 (mp) REVERT: F 333 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7870 (p) REVERT: G 305 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: G 377 ASP cc_start: 0.8371 (m-30) cc_final: 0.8082 (m-30) REVERT: G 475 TYR cc_start: 0.7925 (m-80) cc_final: 0.7691 (m-80) REVERT: G 552 PHE cc_start: 0.8574 (t80) cc_final: 0.8173 (t80) REVERT: a 59 GLU cc_start: 0.8536 (pm20) cc_final: 0.8149 (pm20) REVERT: c 64 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: d 31 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8427 (pttm) REVERT: d 54 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8528 (mmtt) REVERT: f 92 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (ttp80) REVERT: h 39 TYR cc_start: 0.8200 (t80) cc_final: 0.7948 (t80) outliers start: 110 outliers final: 37 residues processed: 406 average time/residue: 1.3304 time to fit residues: 634.7116 Evaluate side-chains 333 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 62 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 230 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN g 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.125076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082988 restraints weight = 60414.495| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.48 r_work: 0.3142 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30424 Z= 0.159 Angle : 0.614 12.145 42559 Z= 0.338 Chirality : 0.037 0.208 4703 Planarity : 0.004 0.059 4180 Dihedral : 26.596 163.514 6813 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.82 % Favored : 93.77 % Rotamer: Outliers : 4.43 % Allowed : 22.93 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2631 helix: 1.71 (0.14), residues: 1467 sheet: -2.15 (0.46), residues: 109 loop : -0.85 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 236 HIS 0.017 0.001 HIS D 18 PHE 0.028 0.001 PHE A 668 TYR 0.018 0.001 TYR B 347 ARG 0.006 0.000 ARG h 76 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 1564) hydrogen bonds : angle 3.73339 ( 4158) metal coordination : bond 0.00795 ( 16) metal coordination : angle 3.32239 ( 9) covalent geometry : bond 0.00354 (30408) covalent geometry : angle 0.61232 (42550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 315 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8798 (m-80) cc_final: 0.8339 (m-80) REVERT: A 719 TRP cc_start: 0.8680 (t60) cc_final: 0.8370 (t60) REVERT: A 723 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8161 (t80) REVERT: A 775 TRP cc_start: 0.7001 (OUTLIER) cc_final: 0.6355 (t-100) REVERT: A 780 ASP cc_start: 0.8418 (t0) cc_final: 0.8137 (m-30) REVERT: A 805 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7970 (mp0) REVERT: A 845 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8686 (pm20) REVERT: A 949 ILE cc_start: 0.8984 (mt) cc_final: 0.8741 (pp) REVERT: A 1149 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8261 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 76 GLN cc_start: 0.8882 (mt0) cc_final: 0.8570 (mt0) REVERT: B 163 LEU cc_start: 0.9001 (tt) cc_final: 0.8782 (tt) REVERT: B 214 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: B 306 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8475 (ttt) REVERT: D 77 PHE cc_start: 0.7543 (m-80) cc_final: 0.6579 (m-80) REVERT: D 78 PHE cc_start: 0.8346 (t80) cc_final: 0.8090 (t80) REVERT: D 226 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7588 (mp) REVERT: D 237 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.3827 (mm-30) REVERT: D 310 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6315 (tp) REVERT: D 320 LEU cc_start: 0.7664 (tp) cc_final: 0.6872 (tp) REVERT: D 376 ASP cc_start: 0.7143 (p0) cc_final: 0.6821 (p0) REVERT: E 23 TYR cc_start: 0.6542 (m-80) cc_final: 0.5938 (m-80) REVERT: E 31 TRP cc_start: 0.3601 (t-100) cc_final: 0.3053 (t-100) REVERT: E 37 MET cc_start: 0.6514 (tpp) cc_final: 0.6235 (tpp) REVERT: E 38 TYR cc_start: 0.6109 (p90) cc_final: 0.5713 (p90) REVERT: E 263 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7163 (t-170) REVERT: E 299 TYR cc_start: 0.3293 (m-80) cc_final: 0.3073 (m-80) REVERT: E 373 TYR cc_start: 0.7432 (m-10) cc_final: 0.6706 (m-10) REVERT: F 333 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (p) REVERT: F 341 PHE cc_start: 0.5847 (m-80) cc_final: 0.5555 (m-80) REVERT: G 164 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6975 (mpt-90) REVERT: G 305 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: G 316 MET cc_start: 0.3804 (tpt) cc_final: 0.2952 (ptt) REVERT: G 377 ASP cc_start: 0.8325 (m-30) cc_final: 0.8083 (m-30) REVERT: G 552 PHE cc_start: 0.8707 (t80) cc_final: 0.8180 (t80) REVERT: G 556 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8391 (m-10) REVERT: a 59 GLU cc_start: 0.8602 (pm20) cc_final: 0.8200 (pm20) REVERT: c 42 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7566 (mtm180) REVERT: c 64 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: d 31 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8413 (pttm) REVERT: d 54 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8510 (mmtt) REVERT: f 92 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8754 (ttp80) REVERT: g 16 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8093 (p) REVERT: h 39 TYR cc_start: 0.8198 (t80) cc_final: 0.7942 (t80) outliers start: 106 outliers final: 40 residues processed: 392 average time/residue: 1.3362 time to fit residues: 615.3461 Evaluate side-chains 336 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 164 ARG Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 42 ARG Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 220 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 270 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 281 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN A1221 HIS ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083774 restraints weight = 59991.742| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.49 r_work: 0.3159 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30424 Z= 0.151 Angle : 0.614 11.265 42559 Z= 0.336 Chirality : 0.037 0.202 4703 Planarity : 0.004 0.053 4180 Dihedral : 26.494 167.140 6809 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.93 % Favored : 93.65 % Rotamer: Outliers : 4.51 % Allowed : 23.52 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2631 helix: 1.75 (0.14), residues: 1468 sheet: -1.79 (0.45), residues: 123 loop : -0.79 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.004 0.001 HIS B 49 PHE 0.030 0.001 PHE A 668 TYR 0.036 0.001 TYR G 372 ARG 0.006 0.000 ARG a 42 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1564) hydrogen bonds : angle 3.66733 ( 4158) metal coordination : bond 0.00693 ( 16) metal coordination : angle 2.93745 ( 9) covalent geometry : bond 0.00334 (30408) covalent geometry : angle 0.61216 (42550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 312 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8780 (m-80) cc_final: 0.8227 (m-80) REVERT: A 719 TRP cc_start: 0.8731 (t60) cc_final: 0.8108 (t60) REVERT: A 775 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6359 (t-100) REVERT: A 780 ASP cc_start: 0.8422 (t0) cc_final: 0.8140 (OUTLIER) REVERT: A 841 MET cc_start: 0.7280 (ptp) cc_final: 0.7072 (ptp) REVERT: A 845 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8701 (pm20) REVERT: A 885 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7552 (mt-10) REVERT: A 949 ILE cc_start: 0.8977 (mt) cc_final: 0.8739 (pp) REVERT: A 978 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: A 1149 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8143 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: A 1255 THR cc_start: 0.8770 (m) cc_final: 0.8504 (t) REVERT: B 73 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: B 76 GLN cc_start: 0.8884 (mt0) cc_final: 0.8600 (mt0) REVERT: B 163 LEU cc_start: 0.8965 (tt) cc_final: 0.8738 (tt) REVERT: B 214 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: D 226 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7598 (mm) REVERT: D 237 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.3804 (mm-30) REVERT: D 310 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6330 (tp) REVERT: D 320 LEU cc_start: 0.7692 (tp) cc_final: 0.6891 (tp) REVERT: D 376 ASP cc_start: 0.7113 (p0) cc_final: 0.6798 (p0) REVERT: E 263 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7092 (t-170) REVERT: E 292 CYS cc_start: 0.7753 (m) cc_final: 0.7451 (p) REVERT: F 316 MET cc_start: 0.6034 (mmt) cc_final: 0.5386 (tmm) REVERT: F 333 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7888 (p) REVERT: G 175 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7331 (ptp) REVERT: G 282 PHE cc_start: 0.8067 (m-80) cc_final: 0.7552 (m-80) REVERT: G 305 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: G 316 MET cc_start: 0.3974 (tpt) cc_final: 0.3131 (ptt) REVERT: G 377 ASP cc_start: 0.8330 (m-30) cc_final: 0.8105 (m-30) REVERT: G 497 LEU cc_start: 0.8267 (tp) cc_final: 0.7785 (pt) REVERT: G 552 PHE cc_start: 0.8689 (t80) cc_final: 0.8136 (t80) REVERT: a 56 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8801 (ttmm) REVERT: a 59 GLU cc_start: 0.8617 (pm20) cc_final: 0.8191 (pm20) REVERT: c 42 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7568 (mtm180) REVERT: c 64 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: d 31 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8491 (pttm) REVERT: d 54 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8520 (mmtt) REVERT: d 120 SER cc_start: 0.8817 (m) cc_final: 0.8616 (p) REVERT: f 53 GLU cc_start: 0.8472 (tp30) cc_final: 0.8153 (tp30) REVERT: f 92 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8760 (ttp80) REVERT: g 16 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8091 (p) REVERT: h 39 TYR cc_start: 0.8208 (t80) cc_final: 0.7909 (t80) REVERT: h 84 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8812 (p) outliers start: 108 outliers final: 43 residues processed: 393 average time/residue: 1.3489 time to fit residues: 623.7606 Evaluate side-chains 349 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 42 ARG Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain h residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 167 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 186 optimal weight: 0.0010 chunk 154 optimal weight: 0.7980 chunk 251 optimal weight: 0.0770 chunk 172 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 974 GLN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085305 restraints weight = 60024.000| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.49 r_work: 0.3188 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30424 Z= 0.139 Angle : 0.612 16.191 42559 Z= 0.333 Chirality : 0.037 0.200 4703 Planarity : 0.004 0.049 4180 Dihedral : 26.367 170.862 6807 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.51 % Favored : 94.11 % Rotamer: Outliers : 3.59 % Allowed : 24.60 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2631 helix: 1.80 (0.14), residues: 1466 sheet: -1.49 (0.45), residues: 132 loop : -0.72 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 236 HIS 0.005 0.001 HIS A 886 PHE 0.035 0.001 PHE E 362 TYR 0.042 0.001 TYR G 372 ARG 0.007 0.000 ARG d 76 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1564) hydrogen bonds : angle 3.61042 ( 4158) metal coordination : bond 0.00575 ( 16) metal coordination : angle 2.33603 ( 9) covalent geometry : bond 0.00304 (30408) covalent geometry : angle 0.61097 (42550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 318 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8726 (m-80) cc_final: 0.8163 (m-80) REVERT: A 719 TRP cc_start: 0.8441 (t60) cc_final: 0.8098 (t60) REVERT: A 723 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 775 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.6493 (t-100) REVERT: A 780 ASP cc_start: 0.8413 (t0) cc_final: 0.8151 (m-30) REVERT: A 805 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8012 (mp0) REVERT: A 841 MET cc_start: 0.7391 (ptp) cc_final: 0.7162 (ptp) REVERT: A 845 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: A 949 ILE cc_start: 0.8954 (mt) cc_final: 0.8725 (pp) REVERT: A 978 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: A 1149 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 1221 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8377 (t-90) REVERT: A 1255 THR cc_start: 0.8816 (m) cc_final: 0.8557 (t) REVERT: A 1268 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 76 GLN cc_start: 0.8882 (mt0) cc_final: 0.8576 (mt0) REVERT: B 214 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: B 306 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8455 (ttt) REVERT: D 77 PHE cc_start: 0.7804 (m-80) cc_final: 0.6975 (m-80) REVERT: D 226 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7606 (mm) REVERT: D 237 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.3865 (mm-30) REVERT: D 310 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6327 (tp) REVERT: D 320 LEU cc_start: 0.7673 (tp) cc_final: 0.6936 (tp) REVERT: D 376 ASP cc_start: 0.7066 (p0) cc_final: 0.6746 (p0) REVERT: E 22 MET cc_start: 0.1050 (mmt) cc_final: -0.0103 (mmt) REVERT: E 263 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7087 (t-170) REVERT: E 288 TYR cc_start: 0.8076 (m-80) cc_final: 0.7806 (m-80) REVERT: E 292 CYS cc_start: 0.7762 (m) cc_final: 0.7545 (p) REVERT: E 373 TYR cc_start: 0.7347 (m-10) cc_final: 0.6588 (m-80) REVERT: F 316 MET cc_start: 0.5968 (mmt) cc_final: 0.5402 (tmm) REVERT: F 333 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7900 (p) REVERT: G 282 PHE cc_start: 0.7987 (m-80) cc_final: 0.7513 (m-80) REVERT: G 305 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: G 316 MET cc_start: 0.3877 (tpt) cc_final: 0.3081 (ptt) REVERT: G 377 ASP cc_start: 0.8314 (m-30) cc_final: 0.8094 (m-30) REVERT: G 497 LEU cc_start: 0.8287 (tp) cc_final: 0.7831 (pt) REVERT: G 550 ASP cc_start: 0.8825 (t0) cc_final: 0.8593 (t0) REVERT: G 552 PHE cc_start: 0.8605 (t80) cc_final: 0.8214 (t80) REVERT: a 56 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8809 (ttmm) REVERT: a 59 GLU cc_start: 0.8618 (pm20) cc_final: 0.8196 (pm20) REVERT: c 64 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: d 54 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8535 (mmtt) REVERT: f 53 GLU cc_start: 0.8460 (tp30) cc_final: 0.8160 (tp30) REVERT: g 16 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7936 (p) REVERT: g 19 SER cc_start: 0.9272 (m) cc_final: 0.9066 (p) REVERT: h 39 TYR cc_start: 0.8177 (t80) cc_final: 0.7892 (t80) outliers start: 86 outliers final: 29 residues processed: 388 average time/residue: 1.3712 time to fit residues: 627.9706 Evaluate side-chains 324 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 178 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1132 ASN A1315 GLN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN h 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080612 restraints weight = 59660.538| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.51 r_work: 0.3091 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30424 Z= 0.217 Angle : 0.658 13.742 42559 Z= 0.358 Chirality : 0.039 0.199 4703 Planarity : 0.005 0.100 4180 Dihedral : 26.798 179.094 6807 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.89 % Favored : 93.73 % Rotamer: Outliers : 3.59 % Allowed : 25.31 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2631 helix: 1.61 (0.14), residues: 1475 sheet: -1.44 (0.45), residues: 132 loop : -0.78 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 236 HIS 0.007 0.001 HIS A 886 PHE 0.032 0.002 PHE A 668 TYR 0.024 0.002 TYR B 347 ARG 0.020 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 1564) hydrogen bonds : angle 3.75462 ( 4158) metal coordination : bond 0.01512 ( 16) metal coordination : angle 3.78240 ( 9) covalent geometry : bond 0.00496 (30408) covalent geometry : angle 0.65597 (42550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 300 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8815 (m-80) cc_final: 0.8245 (m-80) REVERT: A 723 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8337 (t80) REVERT: A 775 TRP cc_start: 0.7004 (OUTLIER) cc_final: 0.6668 (t-100) REVERT: A 780 ASP cc_start: 0.8407 (t0) cc_final: 0.8117 (m-30) REVERT: A 805 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7926 (mp0) REVERT: A 845 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8756 (pm20) REVERT: A 949 ILE cc_start: 0.8991 (mt) cc_final: 0.8752 (pp) REVERT: A 1156 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 1221 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: B 73 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: B 214 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: B 306 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8406 (ttt) REVERT: D 77 PHE cc_start: 0.7869 (m-80) cc_final: 0.7031 (m-80) REVERT: D 226 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7601 (mm) REVERT: D 237 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.3724 (mm-30) REVERT: D 310 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6343 (tp) REVERT: D 320 LEU cc_start: 0.7794 (tp) cc_final: 0.6964 (tp) REVERT: D 376 ASP cc_start: 0.7340 (p0) cc_final: 0.6998 (p0) REVERT: E 22 MET cc_start: 0.1409 (mmt) cc_final: 0.1061 (mmt) REVERT: E 263 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7115 (t-170) REVERT: E 299 TYR cc_start: 0.3747 (m-80) cc_final: 0.3231 (m-10) REVERT: E 373 TYR cc_start: 0.7321 (m-10) cc_final: 0.6556 (m-80) REVERT: F 316 MET cc_start: 0.5869 (mmt) cc_final: 0.5289 (tmm) REVERT: F 319 LEU cc_start: 0.8574 (tp) cc_final: 0.8149 (pt) REVERT: F 333 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7775 (p) REVERT: F 341 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6504 (t80) REVERT: G 305 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: G 377 ASP cc_start: 0.8425 (m-30) cc_final: 0.8116 (m-30) REVERT: G 497 LEU cc_start: 0.8319 (tp) cc_final: 0.7808 (pt) REVERT: G 542 ILE cc_start: 0.8934 (mm) cc_final: 0.8609 (tt) REVERT: G 556 TYR cc_start: 0.8874 (m-10) cc_final: 0.8505 (m-10) REVERT: a 56 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8762 (ttmm) REVERT: a 59 GLU cc_start: 0.8595 (pm20) cc_final: 0.8203 (pm20) REVERT: c 64 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: g 16 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8087 (p) REVERT: h 39 TYR cc_start: 0.8241 (t80) cc_final: 0.7936 (t80) outliers start: 86 outliers final: 40 residues processed: 370 average time/residue: 1.3848 time to fit residues: 600.6888 Evaluate side-chains 325 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 PHE Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 120 optimal weight: 50.0000 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 232 optimal weight: 0.0970 chunk 112 optimal weight: 0.0060 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.125957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084086 restraints weight = 60155.088| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.49 r_work: 0.3165 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30424 Z= 0.146 Angle : 0.642 14.670 42559 Z= 0.346 Chirality : 0.037 0.209 4703 Planarity : 0.004 0.058 4180 Dihedral : 26.486 177.457 6807 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.63 % Favored : 94.03 % Rotamer: Outliers : 3.13 % Allowed : 26.07 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.04 % 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: 0.94 (0.17), residues: 2631 helix: 1.73 (0.14), residues: 1469 sheet: -1.35 (0.45), residues: 133 loop : -0.72 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 236 HIS 0.004 0.001 HIS E 330 PHE 0.041 0.001 PHE E 362 TYR 0.021 0.001 TYR G 372 ARG 0.011 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1564) hydrogen bonds : angle 3.64609 ( 4158) metal coordination : bond 0.00673 ( 16) metal coordination : angle 3.28377 ( 9) covalent geometry : bond 0.00322 (30408) covalent geometry : angle 0.64008 (42550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 TRP cc_start: 0.7156 (OUTLIER) cc_final: 0.6689 (t-100) REVERT: A 780 ASP cc_start: 0.8416 (t0) cc_final: 0.8145 (m-30) REVERT: A 796 ILE cc_start: 0.7400 (pp) cc_final: 0.7095 (pt) REVERT: A 805 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7986 (mp0) REVERT: A 839 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 949 ILE cc_start: 0.8946 (mt) cc_final: 0.8713 (pp) REVERT: A 1156 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: A 1221 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.8293 (t-90) REVERT: A 1300 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7027 (ttp) REVERT: B 73 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: B 214 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: B 306 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8394 (ttt) REVERT: D 77 PHE cc_start: 0.7896 (m-80) cc_final: 0.7053 (m-80) REVERT: D 107 MET cc_start: 0.7728 (ppp) cc_final: 0.7346 (ppp) REVERT: D 226 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7666 (mm) REVERT: D 237 GLU cc_start: 0.4892 (OUTLIER) cc_final: 0.3544 (mm-30) REVERT: D 310 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6343 (tp) REVERT: D 320 LEU cc_start: 0.7735 (tp) cc_final: 0.6975 (tp) REVERT: D 376 ASP cc_start: 0.7251 (p0) cc_final: 0.6886 (p0) REVERT: E 22 MET cc_start: 0.1511 (mmt) cc_final: 0.0835 (mmt) REVERT: E 263 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7051 (t-170) REVERT: E 299 TYR cc_start: 0.3738 (m-80) cc_final: 0.3298 (m-10) REVERT: E 373 TYR cc_start: 0.7329 (m-10) cc_final: 0.6578 (m-80) REVERT: F 316 MET cc_start: 0.5733 (mmt) cc_final: 0.5228 (tmm) REVERT: F 333 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (p) REVERT: F 341 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6704 (t80) REVERT: G 305 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: G 377 ASP cc_start: 0.8371 (m-30) cc_final: 0.8127 (m-30) REVERT: G 497 LEU cc_start: 0.8308 (tp) cc_final: 0.7863 (pt) REVERT: G 550 ASP cc_start: 0.8836 (t0) cc_final: 0.8601 (t0) REVERT: a 56 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8839 (ttmm) REVERT: a 59 GLU cc_start: 0.8610 (pm20) cc_final: 0.8239 (pm20) REVERT: c 64 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: d 54 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8500 (mmtt) REVERT: e 90 MET cc_start: 0.8364 (mmm) cc_final: 0.8153 (mmm) REVERT: f 53 GLU cc_start: 0.8513 (tp30) cc_final: 0.8162 (tp30) REVERT: g 16 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7953 (p) REVERT: h 39 TYR cc_start: 0.8167 (t80) cc_final: 0.7843 (t80) outliers start: 75 outliers final: 35 residues processed: 360 average time/residue: 1.4025 time to fit residues: 599.7427 Evaluate side-chains 331 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 PHE Chi-restraints excluded: chain F residue 341 PHE Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 155 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 293 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 276 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN A1143 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 ASN G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083893 restraints weight = 59387.133| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.48 r_work: 0.3196 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30424 Z= 0.159 Angle : 0.656 12.911 42559 Z= 0.352 Chirality : 0.037 0.213 4703 Planarity : 0.004 0.052 4180 Dihedral : 26.528 178.808 6806 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.85 % Favored : 93.80 % Rotamer: Outliers : 2.59 % Allowed : 26.65 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.04 % 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: 0.96 (0.17), residues: 2631 helix: 1.74 (0.14), residues: 1474 sheet: -1.37 (0.45), residues: 133 loop : -0.69 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 492 HIS 0.005 0.001 HIS B 49 PHE 0.030 0.001 PHE A 668 TYR 0.022 0.001 TYR G 372 ARG 0.016 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 1564) hydrogen bonds : angle 3.63496 ( 4158) metal coordination : bond 0.00795 ( 16) metal coordination : angle 3.23260 ( 9) covalent geometry : bond 0.00356 (30408) covalent geometry : angle 0.65479 (42550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8458 (m-80) cc_final: 0.8236 (m-80) REVERT: A 775 TRP cc_start: 0.7159 (OUTLIER) cc_final: 0.6717 (t-100) REVERT: A 780 ASP cc_start: 0.8497 (t0) cc_final: 0.8246 (m-30) REVERT: A 796 ILE cc_start: 0.7413 (pp) cc_final: 0.7097 (pt) REVERT: A 805 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8054 (mp0) REVERT: A 949 ILE cc_start: 0.8938 (mt) cc_final: 0.8732 (pp) REVERT: A 978 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 1156 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: A 1268 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 1272 ASP cc_start: 0.8270 (t0) cc_final: 0.7949 (p0) REVERT: B 214 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: B 306 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8440 (ttt) REVERT: D 22 MET cc_start: 0.2134 (mmp) cc_final: 0.1831 (mmp) REVERT: D 77 PHE cc_start: 0.7889 (m-80) cc_final: 0.7053 (m-80) REVERT: D 226 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7742 (mm) REVERT: D 237 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.3798 (mm-30) REVERT: D 310 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6563 (tp) REVERT: D 320 LEU cc_start: 0.7767 (tp) cc_final: 0.6967 (tp) REVERT: D 376 ASP cc_start: 0.7216 (p0) cc_final: 0.6863 (p0) REVERT: E 22 MET cc_start: 0.1249 (mmt) cc_final: 0.0708 (mmt) REVERT: E 263 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7049 (t-170) REVERT: E 299 TYR cc_start: 0.3846 (m-80) cc_final: 0.3463 (m-10) REVERT: E 347 MET cc_start: 0.5603 (pmm) cc_final: 0.5182 (ppp) REVERT: E 373 TYR cc_start: 0.7377 (m-10) cc_final: 0.6618 (m-80) REVERT: F 316 MET cc_start: 0.5694 (mmt) cc_final: 0.5157 (tmm) REVERT: F 333 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7768 (p) REVERT: G 268 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: G 305 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 377 ASP cc_start: 0.8409 (m-30) cc_final: 0.8159 (m-30) REVERT: G 497 LEU cc_start: 0.8290 (tp) cc_final: 0.7894 (pt) REVERT: G 542 ILE cc_start: 0.8791 (mm) cc_final: 0.8528 (tt) REVERT: G 550 ASP cc_start: 0.8856 (t0) cc_final: 0.8592 (t0) REVERT: G 552 PHE cc_start: 0.8701 (t80) cc_final: 0.8370 (t80) REVERT: G 556 TYR cc_start: 0.8945 (m-10) cc_final: 0.8643 (m-10) REVERT: a 59 GLU cc_start: 0.8705 (pm20) cc_final: 0.8351 (pm20) REVERT: c 64 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: d 54 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8577 (mmtt) REVERT: e 56 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8717 (ttmm) REVERT: f 53 GLU cc_start: 0.8535 (tp30) cc_final: 0.8179 (tp30) REVERT: h 39 TYR cc_start: 0.8352 (t80) cc_final: 0.8039 (t80) outliers start: 62 outliers final: 36 residues processed: 340 average time/residue: 1.4059 time to fit residues: 558.3120 Evaluate side-chains 322 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 268 GLN Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 248 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 287 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1221 HIS ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 ASN G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084390 restraints weight = 59625.351| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.48 r_work: 0.3206 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30424 Z= 0.154 Angle : 0.657 13.095 42559 Z= 0.353 Chirality : 0.037 0.196 4703 Planarity : 0.004 0.051 4180 Dihedral : 26.461 178.128 6804 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.63 % Favored : 94.07 % Rotamer: Outliers : 2.38 % Allowed : 27.03 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2631 helix: 1.77 (0.14), residues: 1467 sheet: -1.32 (0.44), residues: 134 loop : -0.67 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 492 HIS 0.004 0.001 HIS D 18 PHE 0.047 0.001 PHE E 362 TYR 0.032 0.001 TYR G 372 ARG 0.019 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1564) hydrogen bonds : angle 3.63759 ( 4158) metal coordination : bond 0.00660 ( 16) metal coordination : angle 3.08650 ( 9) covalent geometry : bond 0.00345 (30408) covalent geometry : angle 0.65507 (42550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8458 (m-80) cc_final: 0.8233 (m-80) REVERT: A 775 TRP cc_start: 0.7168 (OUTLIER) cc_final: 0.6712 (t-100) REVERT: A 780 ASP cc_start: 0.8480 (t0) cc_final: 0.8227 (m-30) REVERT: A 796 ILE cc_start: 0.7364 (pp) cc_final: 0.7051 (pt) REVERT: A 805 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8050 (mp0) REVERT: A 978 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: A 1156 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 1268 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 1272 ASP cc_start: 0.8309 (t0) cc_final: 0.7980 (p0) REVERT: B 214 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: B 306 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8435 (ttt) REVERT: D 77 PHE cc_start: 0.7873 (m-80) cc_final: 0.7004 (m-80) REVERT: D 107 MET cc_start: 0.7491 (ppp) cc_final: 0.7042 (ppp) REVERT: D 226 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7710 (mm) REVERT: D 237 GLU cc_start: 0.5145 (OUTLIER) cc_final: 0.3829 (mm-30) REVERT: D 310 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6548 (tp) REVERT: D 320 LEU cc_start: 0.7762 (tp) cc_final: 0.7017 (tp) REVERT: D 376 ASP cc_start: 0.7130 (p0) cc_final: 0.6770 (p0) REVERT: E 22 MET cc_start: 0.1204 (mmt) cc_final: 0.0720 (mmt) REVERT: E 263 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.6993 (t-170) REVERT: E 347 MET cc_start: 0.5632 (pmm) cc_final: 0.4986 (ppp) REVERT: E 373 TYR cc_start: 0.7449 (m-10) cc_final: 0.6682 (m-80) REVERT: F 316 MET cc_start: 0.5650 (mmt) cc_final: 0.5106 (tmm) REVERT: F 333 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7711 (p) REVERT: G 268 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: G 305 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 377 ASP cc_start: 0.8415 (m-30) cc_final: 0.8129 (m-30) REVERT: G 497 LEU cc_start: 0.8285 (tp) cc_final: 0.7898 (pt) REVERT: G 542 ILE cc_start: 0.8755 (mm) cc_final: 0.8473 (tt) REVERT: G 550 ASP cc_start: 0.8845 (t0) cc_final: 0.8590 (t0) REVERT: a 56 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8902 (ttmm) REVERT: a 59 GLU cc_start: 0.8721 (pm20) cc_final: 0.8375 (pm20) REVERT: c 64 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: d 54 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8577 (mmtt) REVERT: e 56 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8715 (ttmm) REVERT: f 53 GLU cc_start: 0.8545 (tp30) cc_final: 0.8201 (tp30) REVERT: h 39 TYR cc_start: 0.8335 (t80) cc_final: 0.8008 (t80) outliers start: 57 outliers final: 37 residues processed: 326 average time/residue: 1.3611 time to fit residues: 520.7592 Evaluate side-chains 321 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 PHE Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 268 GLN Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 294 optimal weight: 0.0970 chunk 224 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 175 optimal weight: 0.0980 chunk 292 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 276 optimal weight: 0.8980 chunk 275 optimal weight: 0.6980 chunk 209 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1165 ASN A1221 HIS ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 ASN G 268 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN d 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.127424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085721 restraints weight = 59694.370| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.50 r_work: 0.3228 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30424 Z= 0.145 Angle : 0.655 12.791 42559 Z= 0.352 Chirality : 0.037 0.228 4703 Planarity : 0.004 0.051 4180 Dihedral : 26.354 177.638 6804 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 2.21 % Allowed : 26.98 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2631 helix: 1.79 (0.14), residues: 1465 sheet: -1.20 (0.43), residues: 144 loop : -0.67 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G 492 HIS 0.005 0.001 HIS A1221 PHE 0.051 0.001 PHE F 326 TYR 0.027 0.001 TYR G 556 ARG 0.019 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1564) hydrogen bonds : angle 3.66114 ( 4158) metal coordination : bond 0.00591 ( 16) metal coordination : angle 2.92468 ( 9) covalent geometry : bond 0.00320 (30408) covalent geometry : angle 0.65347 (42550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24426.56 seconds wall clock time: 419 minutes 58.62 seconds (25198.62 seconds total)